Hi all,
I'm getting counts on __too_low_aQual from htseq-count even when I set the minaqual to zero (--a=0).
no_feature 334...
52 results in 0.0026 seconds.
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__too_low_aQual on htseq-count
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Non-ascii characters in bam file causes htseq-count error
Hello everybody,
I have aligned bam files (using STAR version 2.6.1a_08-27) and want to quantify them using htseq-count (version 0.9.1).... -
Non-ascii characters in bam file causes htseq-count error
Hello everybody,
I have aligned bam files (STAR version 2.6.1a_08-27) and want to quantify them using htseq-count (version 0.9.1). When... -
HTSeq-count returns all 0's?
I am using HTSeq-count to count the number of gene features in my RNA-seq samples. I did the original alignment using HISAT2 with a FASTA file, and the... -
htseq-count ERROR in GFF File?
Hello guys,
I'm trying to do a summary of counts in usegalaxy.org. I convert Fatq groomer to sam with Map with BWA for Illumina (Galaxy... -
Can I use htseq --samout file for subsequent annotation?
Hi,
So briefly what I'm doing is that:
-->I'm annotating my smallRNA sequencing data using htseq-count.
-->I'm using original.sam... -
Single-cell RNA-seq coverage track not corresponding to htseq-count output or IGV
.......... -
htseq-count failure parsing GFF attribute line
Hi,
I am trying to generate a read counts file for my ChIP-seq data using htseq-count. Here is what I have done so far:
1. Call... -
IGV sees many counts, but HTSeq-count counts 0
I appreciate any help to figure out this puzzle.
What I did:
1. I first used tophat2 to map the reads to the genome, get... -
htseq-count __alignment_not_unique vs tophat
Hi guys,
I'm really confused by the numbers between tophat & htseq-count.
There was a huge difference between __alignment_not_unique... -
Difference between Cufflinks coverage and HTSeq-count
Hi,
I am struggling to understand the coverage value (not fpkm) produced by cufflinks. In my case it seems to be much lower than the values... -
Error in htseq-count
Hi all,
I am having a problem when I try to run htseq-count. This is the sentence that I am using:
htseq-count -f bam -s... -
Ambiguous Reads Treatment by HTSeq-Count
Currently, if a person uses HTSeq-Count to count reads on transcript level and the tool finds a read that overlaps two overlapped transcripts (this is... -
samtools sorting issue or HTSeq-count problem?
Hello all,
This has puzzled me for days and I couldnt find any explanation on the internet.
I noticed HTSeq-count gives the reads... -
HTSeq - paired reads count
Hello,
I was wondering if there were any changes in the latest version on HTSeq (after Version 0.5.4) that could affect the count of paired reads...
