Difference between revisions of "Methylation study"
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KangHeum Cho (Talk | contribs) (Created page with "= Tuxedo = == Basic Bowtie2 pipeline == Refer to 2108 Hakyung TUXEDO == HTSeq == Basic command: htseq-count -t exon (-f bam) (--stranded=no) <sorted.bam> <annotation...") |
KangHeum Cho (Talk | contribs) (→HTSeq) |
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== HTSeq == | == HTSeq == | ||
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| + | For detailed information, refer to [https://htseq.readthedocs.io/en/master/count.html HTSeq page]. | ||
Basic command: | Basic command: | ||
Revision as of 06:11, 22 April 2019
Tuxedo
Basic Bowtie2 pipeline
Refer to 2108 Hakyung TUXEDO
HTSeq
For detailed information, refer to HTSeq page.
Basic command:
htseq-count -t exon (-f bam) (--stranded=no) <sorted.bam> <annotation.gff/gtf> > <htseq.txt>
Default input file format is SAM, so specifying '-f bam' for BAM input file is necessary.
For files not following normal HTSeq pipeline, '--stranded=no' option is also required. Refer to 2108 Hakyung TUXEDO.
However, for V. radiata Illumina-sequenced GFF3 files, ID attributes are mixed up, so additional '--idattr' option should be used!
htseq-count -t exon -f bam --stranded=no --idattr transcript_id <sorted.bam> <annotation.gff/gtf> > <htseq.txt>
ID attributes may be:
- transcript_id for GTF format
- Name for GFF format
- etc
