I'm running into a problem with HTSeq that I can't seem to solve on my own:
As running through the entire bam file to find alignments...
55 results in 0.0025 seconds.
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HTSeq.BAM_Reader error: .bam-file has no index ...
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counting wars ;) HTSeq vs RSEM
We have right now an internal lab discussion, a bit of classic "mapper wars" case. What is better, eg in the sense "closer to real biology":... -
GRO-Seq TSS profile plot
Hi everyone,
I have a GRO-Seq NGS dataset (single-end). I would like to plot the average coverage around the TSS (+/- 10Kb) for all the... -
HTseq count for miRNA
Hi,
We did some miRNA sequencing (3 WT vs. 3 condition) and I would like to carry out differential expression analysis using DESeq (DESeq2).... -
htseq-count warning messages: can they be ignored?
Dear all,
I'm new to RNA-seq analysis. I'm Trying out htseq-count to get the raw counts for downstream analysis by EdgeR or DESeq. I am... -
hsteq-count giving zero reads on abundant gene
Dear all and Simon,
htseq-count ran fine on my mm9_transcriptome gtf file. No warning messages.
The output .count file looks... -
Pipeline for DESeq and annotation
Hi, i am new to this and I would like to be able to feed my RNA data into the VST algorithm from DESeq, to normalize my data. But since there is so many... -
htseq-count error with tophat input
Hi all
When using htseq-count with sam-files from tophat and gff files from cufflinks, i got following error:
Error occured in... -
HTSeq-count on bam
Hi!
Is there a way to directly run htseq-count on a bam file? I know that htseq supports bam input via HTSeq.BAM_Reader(), but is there a flag... -
Using HTSeq with Bowtie2 .sam files
Does anyone here use HTSeq to aggregate read counts per gene for their Bowtie2 generated .SAM files? If not, what other method do you use?
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Issue with htseq-count
Hello,
I am working on an RNA-Seq project in soybean. I used Illumina HiSeq for single end reads on my soybean samples and am working on my alignment.... -
installing htseq on a mac
I am trying to install htseq 5.3p9 on my mac (mountain lion, xcode 4.4.1) and i have run into a problem with clang? which i tried googling but am not... -
HTSeq not working with Bowtie2 .SAM
Hi all,
I am having a weird problem with my Bowtie2 .SAM output for use with HTseq to count reads that correspond to genes in a .gff file.... -
HTseq without reference genome
I'm new to RNA-Seq analysis and have Illumina HiSeq paired-end reads (100bp) from plant samples. I would like to get a count of read abundance on the... -
HTseq count to DESeq (?)
Hi all,
I have a little question concerning HTSeq and DESeq.
I am dealing with some bacterial RNAseq data (control + test,...
