Difference between revisions of "Methylation study"
From Crop Genomics Lab.
KangHeum Cho (Talk | contribs) (→HTSeq) |
KangHeum Cho (Talk | contribs) (→HTSeq) |
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Basic command: | Basic command: | ||
− | htseq-count -t exon (-f bam) (--stranded=no) <sorted.bam> <annotation.gff/gtf> > <htseq.txt> | + | htseq-count -t exon (-f bam) (--stranded=no) (-q) <sorted.bam> <annotation.gff/gtf> > <htseq.txt> |
Default input file format is SAM, so specifying '-f bam' for BAM input file is necessary. | Default input file format is SAM, so specifying '-f bam' for BAM input file is necessary. | ||
Line 19: | Line 19: | ||
'''However, for ''V. radiata'' Illumina-sequenced GFF3 files, ID attributes are mixed up,''' so additional ''''--idattr'''' option should be used! | '''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> | + | htseq-count -t exon -f bam --stranded=no -q '''--idattr transcript_id''' <sorted.bam> <annotation.gff/gtf> > <htseq.txt> |
ID attributes may be: | ID attributes may be: |
Revision as of 07:20, 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) (-q) <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 -q --idattr transcript_id <sorted.bam> <annotation.gff/gtf> > <htseq.txt>
ID attributes may be:
- transcript_id for GTF format
- Name for GFF format
- etc