mapping-illumina~HISAT2

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).

input_1:paired-end FASTQ(.gz) files

input_1/SRR4425244_1.fastq

@SRR4425244.1 1 length=101
CTGTNCTACTCCATCGTTGAAAATCTCGCCATTGGGAACTTGAGGCGCAGGAAGGGGCAGCTCCTCAACTGGCAACACTGGTTCCGGTACAACCGGATCTA
+SRR4425244.1 1 length=101
@@@D#2ADFHHHDGII@GHIIIFGIIIIGIIEGEBFHIIIIEGIIIIHIIGEHFDBECCC@CCCACCCCCACBCABBBCCBCCCC995>BCC:<@B<BBCC
@SRR4425244.2 2 length=101
CCCGCATTCCATTGCCAATGGTTTCAAGAACCTTTTGGCCATCGCTGCTGTCACAGAGGTTGAGTTTGAAGAAGCTACCACCATCAAGGAGTTCATTAAGN
+SRR4425244.2 2 length=101
?@@DBDDFDFADHGGIIICCG:BFHIIGE;EFBGHIGGGGIGGGIHIIIH=BGBDGEHG=@GGG=EHH;;3?C);;?>>@C?B@CCCCCBBCAAC>C@AC=
@SRR4425244.3 3 length=101
AAACTCCAGGCTTAAAAGCAATTTTTATAAAAAAAAATACAAGTAGAATAAAAAAAGAGCTTTGTTGCCCGTTTTTTCAAAAGTAACAAATTGTATCATAT

input_1/SRR4425244_2.fastq

@SRR4425244.1 1 length=101
CCTGAACCTGTTTTCCCGGTGGAACCATCTGAACCTGTCGTCCCCGTAGAACCATCTGAACCTGTTATCCCCGTGGAACCTGAGCCCATCGATAATCCTTC
+SRR4425244.1 1 length=101
@C@FFDFFHHDFDGIIIIA@FHGGGJIJHGIIJBHEHFHCDGHDGF<8FHFHGICHFHHEHFBD?CCCCEEC83;@@CCB<9?<CAB?CC@9?BBCACC4:
@SRR4425244.2 2 length=101
CGCTTTCTTCCTCCTCTTTTTCTTCTTTCTTTTCCTCCTTCTTCTCAGCCGGAGCAGCGGCGGCGGACGGTGCCACCGCGGCAGCAACTGCAGCGAACTTT
+SRR4425244.2 2 length=101
B@@FFFADHHFHGGIEI>AHF?FH@HHIJFDHIHEH?BGHBFD<BBI@BF@HG<FH>D</:9?=>B-80;&2-9>:<><95-&0<?A839@##########
@SRR4425244.3 3 length=101
GAATGATTAAAATACAATAAATTGAAGACGTGAGTGGATGAAGGGATATGATACAATTTGTTACTTTTGAAAAAACGGGCAACAAAGCTCTTTTTTTATTC

input_1/SRR4425245_1.fastq

@SRR4425245.1 1 length=100
AATTTAGAATCAACATGATTTGCAGAGTTTAAAGAATCAAAACGAATCGAGTAATTTTACTCATTTGAGATCCGTGCTTCTAGCACAACCAGTCTTCCAN
+SRR4425245.1 1 length=100
@<?;?BBDBF<DFFHHII<FHD9CF@FH@HGGCH@>BAGCGD@F??:8?BFDFGIGGGGGGIGG;FHC=DCG>G?;8?;?;CBCC>ACBBBB5A@CAAA:
@SRR4425245.2 2 length=100
NCCTAGTCCAGCGTCATCGTCTCCATTTCCATGCCCATGTCCATGAACTCCAATACCAGCACCAACTCCTAGTCCAGCGTCATCGTCTCCATTTCCATGC
+SRR4425245.2 2 length=100
#1=DFFFFHHGHHJJIJJJGIHIIIJJIGEGIGIIIEE;DGIIJIJIJIIJJIHIGHIHIHIJIIJGHIFEH=CEB?DCABDDDDDDDDDDDEEEDDDCC
@SRR4425245.3 3 length=100
TTTACATACAATAAATTTTATCAAGCAATTTTTAAGTCTTAGTATTTTCTCAATTATCAATTTGAAAAATTTGTTAATTGTCTCTATATAGTAAAATCCA

input_1/SRR4425245_2.fastq

@SRR4425245.1 1 length=100
CTCGGTTCGGTTAGGAAATATCAGGGTCTGGAAGACTGGTTGTGCTAGAAGCACGGATCTCAAATGAGTAAAATTACTCGATTCGTTTTGATTCTTTAAA
+SRR4425245.1 1 length=100
?BBF?+@DFFA8CFBEFEGGHGIIEIGAFGEIGIBB@<DFFG?DGG@48CDGGDH8;A4?;=>D;BBB>A>;>;>C@;@==CCC@CCDDD?CDDDDD###
@SRR4425245.2 2 length=100
CTAGGACTAGGTATTGGTGCCGGAATTCATGGACATGAACATGGAAATGGAGACGGTAACGCTGAGCTAGGAGTTGGTGCTGGTGTTGGAGTTCATGGAC
+SRR4425245.2 2 length=100
@CCFFDFFDHHAFGGIJIJJIJJJIJJJJIIIEGIIIJIJJIIJJIIHJJJGHGIIHCEDEEHFDFFFDEE>A@CCD;?CDDD,<<?BA@C@CD@CDDCD
@SRR4425245.3 3 length=100
CGAAAAAGAAAACTTTTTGAAATTGGCAGTGAGAGTGAAATACAGTGGATTTTACTATATAGAGACAATTAACAAATTTTTCAAATTGATAATTGAGAAA

input_1/SRR4425248_1.fastq

@SRR4425248.1 HWI-ST576R:222:D1K09ACXX:1:1101:1214:2066 length=100
TCTAATCCAAAGTCACAGATATCGTACTGTATATAACTGGTCATTAAAATAGTTCCTTGCGCTTCAAATACTTCTTGAAGACTAACCGCGATGTTGTTCA
+SRR4425248.1 HWI-ST576R:222:D1K09ACXX:1:1101:1214:2066 length=100
@CCFFFFFHHHHDGGIJJJIIIHICFGIJAFHIEIGEEHICHHJJEHGIIDFBBFHIIHI>FHGHHICFHHHGHIHGHFEHFFCCBEDDDDDDA@C?BD@
@SRR4425248.2 HWI-ST576R:222:D1K09ACXX:1:1101:1206:2097 length=100
AAACTCTTGGCATAACGGCCTTGCACATAAAGCTCCGTGCTACTGGTGGAAACAAAACAAAGACCCCTGGTCCTGGTGCTCAGTCTGCACTTCGGGCTCT
+SRR4425248.2 HWI-ST576R:222:D1K09ACXX:1:1101:1206:2097 length=100
@@@FFFFFHGHFHJJJHIBHGIIHGIJEIJIGGHIIJBGHIIJJJJGHIDCFFCHJJIJJIHGCEEFFFDEEECDD5=C>CCDACDDDADDDDDDDBDDD
@SRR4425248.3 HWI-ST576R:222:D1K09ACXX:1:1101:1178:2178 length=100
ATGCTACGCCAGAGTCTACATGAACCAGGGAATGTTCTTATACGCCTACTACATAGCTATTATCCAGCGCTCTGACACCGCCAGCTTCGTTCTACCTGCT

input_1/SRR4425248_2.fastq

@SRR4425248.1 HWI-ST576R:222:D1K09ACXX:1:1101:1214:2066 length=100
NACAAAGTCAGTTAGGCAAGCTGCTGAACAACATCGCGGTTAGTCTTCAAGAAGTATTTGAAGCGCAAGGAACTATTTTAATGACCAGTTATATACAGTA
+SRR4425248.1 HWI-ST576R:222:D1K09ACXX:1:1101:1214:2066 length=100
#1=DDFFDHHHHHJJJIIJIJIFJJJJJEHHHIFCEHIIHIFEDFHIIEICHIJ@FHIIEGJIJGHFFDDEEBCDDDEEDDDDDDDDDCC@CDDEEE@4>
@SRR4425248.2 HWI-ST576R:222:D1K09ACXX:1:1101:1206:2097 length=100
GTGACATCTTCAATGCGGCCAATCTTCATACTTGAACGAGCAAGAGCCCGAAGTGCAGACTGAGCACCAGGACCAGGGGTCTTTGTTTTGTTTCCACCAN
+SRR4425248.2 HWI-ST576R:222:D1K09ACXX:1:1101:1206:2097 length=100
CCCFFFFFHHHHHJJIIJGIJJFIJIJJIJJJJJJJJIGIJJGHJIJJIGGII;EHGHFFFFDCCEDDBDDBBBBABDD09CCDDACDDDBDDDDEDDBD
@SRR4425248.3 HWI-ST576R:222:D1K09ACXX:1:1101:1178:2178 length=100
TTATAACATATTTTCTCGTCAAGGCAACCATCCATCATCTTAACGTAGGCCATTTTATTTTTAACTTCCATGTTGACAAAATATTGAGGATAAGCTTCGT

input_1/SRR4425249_1.fastq

@SRR4425249.1 1 length=101
NGTATTTTCCCGTTTTCCAGTTAATTAAGTTTCTATCTAAAAGCACTATGCAGTGTTCTCGAGTTAAAGTAGCGTTTTTATTTTTATCTGTTTTACCATGN
+SRR4425249.1 1 length=101
#14ADFFFHHHHHJJJJJGIHIIIJIIJJHIIJJJJJJJJJJIEHIJJJJJJJDHFCFIJJDHFHGGGI;FHIIIHHHHFFFFFFDEEEECDDDDCDDDDA
@SRR4425249.2 2 length=101
NAGAAGCTGGCCGATGGCTACGACCTAACGGCGGAACTGGACAAAATGTTCTCGACCAAAGTGCGAGTGACGGTGCCGAAATTCAAGATCGAAACTGANNN
+SRR4425249.2 2 length=101
#1:DDDDDFBAHDGGHIEFHIBFGIIIIIGGH<AED6@ECAACCCBCC>CDCC?AB@B?B?3>@@>;)2@CBB5ABC<@@BACCCDCCCCB?C@BCCCCCC
@SRR4425249.3 3 length=101
CAGAACCTAGTTCATACCAGGTGTACCAGATATGGTTTGCCTAGTGACGAATGTGCGAGTTTCATCAGCACGTTAAACTTACGCGAGACCGATTTTGANNN

input_1/SRR4425249_2.fastq

@SRR4425249.1 1 length=101
CTTTGTTACCCCACAACTCGTTTGAGAAACATTTGTTTTCTTTTATACACCACGAGCATTGGGATAATTTCAAACAATCAAAACATGAGACCTTAACAGCA
+SRR4425249.1 1 length=101
@@CFFEFDHHHHGJJIJHIJIJJJJJJJJIJJJJJIJJIIJJJJJ?FHJJHHIHIJJJJJJJHHHHFFFFFFFFEEDEEDDDDDDCCDDDDDDDDCDDCDC
@SRR4425249.2 2 length=101
GGAAGCTCGGCGAAGGCGGGCGGGCGCACCGCATCATCATCACCATGCCTGTGGCGGCGGCTGCTTTGGCGCCTTCCTCGTTGACTTCAATGAAGGCTTTT
+SRR4425249.2 2 length=101
?@@FD<DDHDFFHIIIIB@AH?@DDDD@BB@DDDBDDDDB>C@CCCCCC>>9A<B8B############################################
@SRR4425249.3 3 length=101
CAAAATCGGTCTCGCGTAAGTTTAACGTGCTGATGAAACTCGCACATTCGTCACTAGGCAAACCATATCTGGTACACCTGGTATGAACTAGGTTCTGANNN

input_1/SRR4425250_1.fastq

@SRR4425250.1 HWI-ST576R:236:C1PFUACXX:7:1101:1597:2081 length=101
GTGGNCTCGGAAATCTCAAACTTCAAGCATTTTTATTCAAGCATTCGTCATTCTATAGATAAATGTCGCCGGTACCCGAATACAGTCAGAGCAATTTAAGT
+SRR4425250.1 HWI-ST576R:236:C1PFUACXX:7:1101:1597:2081 length=101
@=?D#2=DHHHDHJJJJJIJJIIJGFHEFGHIJJJJJIGIJJJJJJIIIJJGIHHJDIIIJJJCH@FHHGIF=>CCCDDDDDDDDCCCDCCDDD@CCDDC@
@SRR4425250.2 HWI-ST576R:236:C1PFUACXX:7:1101:1651:2201 length=101
GGCTCATATCTCAAGGTAGGGGGCGGCATTTACGTTGTAGATATCTATGGGCTCCGGTAACCACTTAACACCAGGTGGATCATGAGCTCGACCATCCAGTA
+SRR4425250.2 HWI-ST576R:236:C1PFUACXX:7:1101:1651:2201 length=101
@;?DDDDDDD?CC?BB22A1C6FAFA6BBEE>D?;@?@9;;@5>;>>>AA?BBBBBB0;<A@:8AABBBB3?2<?4>?8>@@@>@AB>@3&000498:@##
@SRR4425250.3 HWI-ST576R:236:C1PFUACXX:7:1101:1669:2215 length=101
ACTTGCTTCACTCTATCGTCAAGTGTGACGGGTTGTTTGCGTGTTGTGCCATCAATGAATTTGTACCATCAACAGGTGTCTAACTCCGCTCAATCGTTACT

input_1/SRR4425250_2.fastq

@SRR4425250.1 HWI-ST576R:236:C1PFUACXX:7:1101:1597:2081 length=101
CCTAAGTGACGGTGTTAACGAACCAATTTCAACATTTGCCATTCTGTCGACTGCACACTTAAATTGCTCTGACTGTATTCGGGTACCGGCGACATTTATCT
+SRR4425250.1 HWI-ST576R:236:C1PFUACXX:7:1101:1597:2081 length=101
@BCFDFDDHHHHCFFDGIIEHIJJJGHHIIGGF?DGGIIIJIJIIJFHGIGGIIJJJJIJJJJHHGHGGFDEFFF>BCACCBD;;>ADDDDBDBB@BCDDC
@SRR4425250.2 HWI-ST576R:236:C1PFUACXX:7:1101:1651:2201 length=101
AAAAAAAGGAAAGCCCTTCTGAAAATCAAATTGCTGATTCTAATCCAGAATGTGATATGGAAGGTAATATGAAACAAAGCCTCCATTGCCGAATTCATCAA
+SRR4425250.2 HWI-ST576R:236:C1PFUACXX:7:1101:1651:2201 length=101
?B<71A?@ADFH>BEHIGFGGHIIIGGHIIIJEI9GFDFHIEGIIG?FHH@>8=C>AACGEHAC..=?EEEFDEFFFDCEEDD@?CC3;@BBBD?CAAD@@
@SRR4425250.3 HWI-ST576R:236:C1PFUACXX:7:1101:1669:2215 length=101
CATTGTTATTGCAGTCTGTTGCGGCGGCCCCACCGCCCACATGTCACAAGAAGGCGTGATGAAACGCGGCCGGCCGCGCCTCCGTATTACGGTCCACCAAC

input_1/SRR4425251_1.fastq

@SRR4425251.1 HWI-ST576R:236:C1PFUACXX:7:1101:1643:2178 length=101
GCCCTTCAAGCCGTAACGCTTTACTGCGAATTACTGCTTCACGGCAGAAAAAGGCAGGGCGATGGTACCTACCAGTGGGAACTTACAAGACGTCCTACGCT
+SRR4425251.1 HWI-ST576R:236:C1PFUACXX:7:1101:1643:2178 length=101
@@@DDDDDHFBHFFF<FA<;F=<F@EC?C:F@F@EE>GDEHHIBGGB@EGG=8-66?AA?8;;=?5>(:(:??:ACC(+8><C3>CCC@<?@#########
@SRR4425251.2 HWI-ST576R:236:C1PFUACXX:7:1101:1690:2200 length=101
GCATGTTTACATACTGTTTATTTATCTGACTTAAAGATACAAAATGGGTTACAAACACCAATAGATAATTAACACTAATAGATAACAAACATAAACTTTNN
+SRR4425251.2 HWI-ST576R:236:C1PFUACXX:7:1101:1690:2200 length=101
BCCFFDDFHHHHHJJJHJIGIJJIIIJJGIIIIJJ>HIIJGIJJIJJIGHIJJJJJIJJIJJIEIIJJJJJJJJJIHIIHHHHHHFFCDFCDECEEDDDDC
@SRR4425251.3 HWI-ST576R:236:C1PFUACXX:7:1101:1708:2217 length=101
GCGTGTTTACATACTGTTTATTTATCTGACTTAAAAATACAAAATGGGTTACAAACACCAATAGATAATTAACACTAATAGATAACAAACATAAACTTTNN

input_1/SRR4425251_2.fastq

@SRR4425251.1 HWI-ST576R:236:C1PFUACXX:7:1101:1643:2178 length=101
ATTGTAAATAAACCTGAAAATACACTATGAATGAGCGAGCGTAGGACGTCTTGTAAGTTCACACTGGTAGGTACCATCGCCCTGCCTTTTTCTGCCGTGAA
+SRR4425251.1 HWI-ST576R:236:C1PFUACXX:7:1101:1643:2178 length=101
B@CFBDEDHHHHGJIJIIJE@IGJJJJGHIGHIGIIJIEIIHHFHGHI@GFHHCEHGIGEECEEECD@DFD;@CEEECDDDD;?BDDC@ACCDCCDDDBDD
@SRR4425251.2 HWI-ST576R:236:C1PFUACXX:7:1101:1690:2200 length=101
GAAAATAGATGATCAGAGAAGGCGTACTTATGATAGGAAACATTAATTACTTGTTAGTGAAATTTTTTGGTGTAGGCTGTCTTTTAGTATGAAAAGCAATT
+SRR4425251.2 HWI-ST576R:236:C1PFUACXX:7:1101:1690:2200 length=101
CCCFDFFFHHHGHJIJIIIGGGIJHJJJJJJJIGIJJIJJJIJJJJGIHJJJIHICHCGGIIIJJJIIEHCDDFFFAEEEEDDDCCDDEFEDEDDDDDDDD
@SRR4425251.3 HWI-ST576R:236:C1PFUACXX:7:1101:1708:2217 length=101
GAAAATAGATGATCAGAGAAGGCGTACTTATGATAGGAAACATTAATTACTTGTTAGTGAAATTTTTTGGTGTAGGCTGTCTTTTAGTATGAAAAGCAATT

input_2:reference genome file (reference genome or index is needed)

input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa

>Bomo_Chr1
CTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAAC
CTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAAC
CTAACCTAATAACCTAACCTAACCTAACCTAACCTTAACCTAACCTAACCTAACCTAACCTAACCTAACC
TAACCTAACCTAACCTAACCTAACCTACCTTAACCTAACTAACCTAACCTAACCTAACCTAACCTAACCT
AACCTAACCTAAACCAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCT
AACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCT
AACCTTAACCTAACCTAACCTAACCTAACCTAACCAACCTAACCTAACCTAACCTAACCTAACCTAACCT
AACCTAACCTAACCTAACCTAACCTAAAACCTAACCTAACCTAACCTAACCTAACCTAACCTAACCTAAC
CTAACCTAACCTAACCTAACCTAACTAACCTAACCTACCTAACCTAACCTAAACCTAACCTAACCTAACC

input_3:reference gene model file (gtf or gff3) [optional]

input_3/Bomo_gene_models.withnote.plus.NC_002355.gff3

##gff-version   3
Bomo_Chr1	.	gene	20596	24779	0.13	+	.	ID=KWMTBOMO00001;Name=KWMTBOMO00001;Note=PREDICTED:_uncharacterized_protein_LOC106648510_[Trichogramma_pretiosum]
Bomo_Chr1	.	mRNA	20596	24779	0.13	+	.	ID=KWMTBOMO00001.mrna1;Name=KWMTBOMO00001;Parent=KWMTBOMO00001
Bomo_Chr1	.	transcription_start_site	20596	20596	.	+	.	Parent=KWMTBOMO00001.mrna1;
Bomo_Chr1	.	exon	20596	21325	.	+	.	ID=KWMTBOMO00001.mrna1.exon1;Parent=KWMTBOMO00001.mrna1;
Bomo_Chr1	.	start_codon	20692	20694	.	+	0	Parent=KWMTBOMO00001.mrna1;
Bomo_Chr1	.	CDS	20692	21325	0.44	+	0	ID=KWMTBOMO00001.mrna1.CDS1;Parent=KWMTBOMO00001.mrna1
Bomo_Chr1	.	initial	20692	21325	0.44	+	0	Parent=KWMTBOMO00001.mrna1;
Bomo_Chr1	.	intron	21326	21564	0.22	+	.	Parent=KWMTBOMO00001.mrna1;
Bomo_Chr1	.	CDS	21565	24719	0.31	+	2	ID=KWMTBOMO00001.mrna1.CDS2;Parent=KWMTBOMO00001.mrna1

input_3/Bomo_gene_models.withnote.plus.NC_002355.gtf

NC_002355.1	stdin	transcript	15095	15883	.	+	.	gene_id "gene-COX3"; transcript_id "cds-NP_059480_1";  gene_name "gene-COX3";
NC_002355.1	stdin	exon	15095	15883	.	+	.	gene_id "gene-COX3"; transcript_id "cds-NP_059480_1"; exon_number "1"; exon_id "cds-NP_059480_1.1"; gene_name "gene-COX3";
NC_002355.1	stdin	CDS	15095	15880	.	+	0	gene_id "gene-COX3"; transcript_id "cds-NP_059480_1"; exon_number "1"; exon_id "cds-NP_059480_1.1"; gene_name "gene-COX3";
NC_002355.1	stdin	start_codon	15095	15097	.	+	0	gene_id "gene-COX3"; transcript_id "cds-NP_059480_1"; exon_number "1"; exon_id "cds-NP_059480_1.1"; gene_name "gene-COX3";
NC_002355.1	stdin	stop_codon	15881	15883	.	+	0	gene_id "gene-COX3"; transcript_id "cds-NP_059480_1"; exon_number "1"; exon_id "cds-NP_059480_1.1"; gene_name "gene-COX3";
NC_002355.1	stdin	transcript	14403	15080	.	+	.	gene_id "gene-ATP6"; transcript_id "cds-NP_059479_1";  gene_name "gene-ATP6";
NC_002355.1	stdin	exon	14403	15080	.	+	.	gene_id "gene-ATP6"; transcript_id "cds-NP_059479_1"; exon_number "1"; exon_id "cds-NP_059479_1.1"; gene_name "gene-ATP6";
NC_002355.1	stdin	CDS	14403	15077	.	+	0	gene_id "gene-ATP6"; transcript_id "cds-NP_059479_1"; exon_number "1"; exon_id "cds-NP_059479_1.1"; gene_name "gene-ATP6";
NC_002355.1	stdin	start_codon	14403	14405	.	+	0	gene_id "gene-ATP6"; transcript_id "cds-NP_059479_1"; exon_number "1"; exon_id "cds-NP_059479_1.1"; gene_name "gene-ATP6";
NC_002355.1	stdin	stop_codon	15078	15080	.	+	0	gene_id "gene-ATP6"; transcript_id "cds-NP_059479_1"; exon_number "1"; exon_id "cds-NP_059479_1.1"; gene_name "gene-ATP6";

input_3/Bomo_gene_models.withnote.plus.NC_002355.withname.gtf

NC_002355.1	stdin	transcript	15095	15883	.	+	.	gene_id "gene-COX3"; transcript_id "cds-NP_059480_1"; gene_name "COX3";
NC_002355.1	stdin	exon	15095	15883	.	+	.	gene_id "gene-COX3"; transcript_id "cds-NP_059480_1"; exon_number "1"; exon_id "cds-NP_059480_1.1"; gene_name "COX3";
NC_002355.1	stdin	CDS	15095	15880	.	+	0	gene_id "gene-COX3"; transcript_id "cds-NP_059480_1"; exon_number "1"; exon_id "cds-NP_059480_1.1"; gene_name "COX3";
NC_002355.1	stdin	start_codon	15095	15097	.	+	0	gene_id "gene-COX3"; transcript_id "cds-NP_059480_1"; exon_number "1"; exon_id "cds-NP_059480_1.1"; gene_name "COX3";
NC_002355.1	stdin	stop_codon	15881	15883	.	+	0	gene_id "gene-COX3"; transcript_id "cds-NP_059480_1"; exon_number "1"; exon_id "cds-NP_059480_1.1"; gene_name "COX3";
NC_002355.1	stdin	transcript	14403	15080	.	+	.	gene_id "gene-ATP6"; transcript_id "cds-NP_059479_1"; gene_name "ATP6";
NC_002355.1	stdin	exon	14403	15080	.	+	.	gene_id "gene-ATP6"; transcript_id "cds-NP_059479_1"; exon_number "1"; exon_id "cds-NP_059479_1.1"; gene_name "ATP6";
NC_002355.1	stdin	CDS	14403	15077	.	+	0	gene_id "gene-ATP6"; transcript_id "cds-NP_059479_1"; exon_number "1"; exon_id "cds-NP_059479_1.1"; gene_name "ATP6";
NC_002355.1	stdin	start_codon	14403	14405	.	+	0	gene_id "gene-ATP6"; transcript_id "cds-NP_059479_1"; exon_number "1"; exon_id "cds-NP_059479_1.1"; gene_name "ATP6";
NC_002355.1	stdin	stop_codon	15078	15080	.	+	0	gene_id "gene-ATP6"; transcript_id "cds-NP_059479_1"; exon_number "1"; exon_id "cds-NP_059479_1.1"; gene_name "ATP6";

input_4:reference index file [optional] (reference genome or index is needed)

input_4/hisat2_index.1.ht2

input_4/hisat2_index.2.ht2

input_4/hisat2_index.3.ht2

input_4/hisat2_index.4.ht2

input_4/hisat2_index.5.ht2

input_4/hisat2_index.6.ht2

input_4/hisat2_index.7.ht2

input_4/hisat2_index.8.ht2

Option

-c "8" -m "64" -p "-trim_tail_right 5 -trim_qual_right 20 -ns_max_p 20 -min_len 30 -trim_qual_window 5" -b "" -i ""

Output

output.sorted_bam

view all outputs