Hello,
I'm new to working with RNAseq data and have a question about counting reads with HTSeq.
I have stranded data that...
55 results in 0.0026 seconds.
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Majority of reads counted in stranded=reverse using HTSeq?
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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... -
Error in htseq-count. Large gaps in CIGAR string
Hi,
I am getting this error when I run htseq-count (version 0.5.4p3)
Error occured in line 6684695 of file OUT.gsnap.combined.Control_72_Rep3_R1.fastq.uniq.... -
HTSeq Counting Warning
Hello
I am getting lots of warning messages when I run HTSeq-count. I saw few other posts on this forum, but could not figure out the solution.... -
DESeq on 4 conditions, 3 replicates each - how?
Hello,
I am a bench developmental biologist with essentially 0 bioinformatics background, so please excuse my stupidity.
... -
HTSeq exon counts to gene level
Hi,
I'm working with drosophila melanogaster RNA-Seq data and at least one of my genes of interest is overlapping an other gene so I used... -
DESeq: question about using HTSeq counts
In the count files from HTSeq there are a few lines at the end:
__no_feature
__ambiguous
__too_low_aQual
__not_aligned... -
How to iterate over reads in file with HTSeq?
I am currently attempting to write a program in Python (v2.7.6) and am using HTSeq to read in fastq files and then run my code on it. However my issue... -
Counts on single and paired ends reads merged bam file
Dear all,
We have made experiments either paired-end AND single-end on the same sample. Next, the 2 corresponding BAM files has been merged, making... -
Which tool should I use to summarize counts from BWA-mem?
From what I read, BWA-mem is one of the best alignment tools (at least for de novo transcriptomes).
However, it seems that summarization... -
Sorted bamfiles have increased size!!
BACKGROUND:
I have RNA-Seq data from Illumina platform.
I aligned the reads post-QC onto hg19 bowtie index using tophat.
Now I wished... -
problem with HTSeq
hi everyone
I'm trying to start to use python/HTSeq to try to analyse RNA seq data.
I'm following a tour through HTSeq but i m... -
Getting started with DESeq2
Hello everyone,
I'm trying to run DESeq2 package on R Studio under Wondows8 and I just can't do it right even if I've successfully used... -
HTSeq issue with stdout/stdin
Hello All,
I like to apply HTSeq-count on a .bam file, but if I directly pipe the output of samtools to htseq it gives me an error. However,... -
Error in HTSEQ
Hi everyone,
I am using the latest version of GSNAP to get alignments for 29 RNAseq samples. So after I get a SAM alignment from GSNAP, I...Last edited by komalsrathi; 10-24-2013, 10:29 AM.
