Methylation study
From Crop Genomics Lab.
Revision as of 06:11, 22 April 2019 by KangHeum Cho (Talk | contribs)
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