Difference between revisions of "Methylation study"

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(HTSeq)
(HTSeq)
Line 11: Line 11:
 
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