Merge pull request #2691 from mblue9/de_novo_fix

bgruening · web-flow · commit 92f085b14c5b · 2021-06-29T12:19:52.000+02:00
de novo: perform paired-end counting with featurecounts
diff --git a/topics/transcriptomics/tutorials/de-novo/tutorial.md b/topics/transcriptomics/tutorials/de-novo/tutorial.md
@@ -254,6 +254,8 @@ The recommended mode is "union", which counts overlaps even if a read only share
 >    - *"Specify strand information"*: `Stranded (Forward)`
 >    - {% icon param-file %} *"Gene annotation file"*: `in your history`
 >       - *"Gene annotation file"*: `the annotated transcripts GTF file output by GFFCompare`
+>    - *"Options for paired-end reads"*
+>       - *"Count fragments instead of reads"*: `Enabled; fragments (or templates) wil be counted instead of reads`
 >    - *"Advanced options"*
 >       - *"GFF gene identifier"*: `transcript_id`
 >

Original file line number	Diff line number	Diff line change
`@@ -254,6 +254,8 @@ The recommended mode is "union", which counts overlaps even if a read only share`
`254`	`254`	> - "Specify strand information": `Stranded (Forward)`
`255`	`255`	> - {% icon param-file %} "Gene annotation file": `in your history`
`256`	`256`	> - "Gene annotation file": `the annotated transcripts GTF file output by GFFCompare`
	`257`	`+> - "Options for paired-end reads"`
	`258`	+> - "Count fragments instead of reads": `Enabled; fragments (or templates) wil be counted instead of reads`
`257`	`259`	`> - "Advanced options"`
`258`	`260`	> - "GFF gene identifier": `transcript_id`
`259`	`261`	`>`