htseq for specific features
Hello,
I have a bed file with genomic ranges. I would like to use htseq to count reads from my bam file that mapped to these particular regions.
Could you please let me know how I can do that with htseq ?
Thanks J
• 2,078 views
•
link
written
by
simonjean434 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
quantify counts from sorted bam files using a bed file containing regions of interest
written by bioyas •
-
Bam file metrics
written by Sabeen •
-
Soft-clipping of a BAM file based on regions from the BED file
written by lechu •
-
is 0-based start and 1-based end of bed format not compatible with htseq-count?
written by Zee_S
-
How to get regions with mapped reads
written by nanoide
-
Get the regions mapped by the same reads
written by Corentin
-
How to find out whether Chip-seq peaks falls within promoter or enhancer region of gene?
written by crazyscientist •
-
Problems getting read number per gene after sequencing
written by ThePresident
-
Combine regions of an interaction matrix
written by bharath.mh24 •
-
Single-cell RNA-seq coverage track not corresponding to htseq-count output or IGV gene annotations?
written by shanasabri •
Why not use bedtools instead?
or ( along with beddtools ) you could use featureCounts instead of htseq-count unless there are overlapping ambiguous regions.