37 results in 0.0025 seconds.
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HTSeq-count: proper pairs in bam file
I have human RNA reads that I aligned against the human reference genome (GRCh 38) using BWA MEM and TopHat2. I now want to count the genes with HTSeq-count.... -
bash loop to count multiple words from multiple corresponding files
I have generated multiple read mapping files (.sam) generated with bowtie2 "--no-unal" parameter. As the number of files are huge (7 reference... -
ht seq counting/ Most of reads into alignment non unique
Hi all,
I am new to Rna seq. I am runnign ht seq within galaxy but at the end most of my reads end up in alignment non unique
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Htseq_processing double number of aligned reads
Hi All,
I am trying to generate count data from the bam files using Htseq. Our data was produced using Illumina stranded library and sequenced... -
HTSeq and repeated exons
Does anyone know how htseq-count handles reads that map to an exon that is found in two alternative transcripts of the same gene? That exon will be repeated... -
Issue with Htseq-count on BAM files from Tophat2 using Galaxy
Hello,
I'm currently facing troubles using galaxy. I want to compare differentially expressed genes between two treatment groups. I already... -
Bowtie to analyze miRNA
Hi everyone,
I have 50 bp single end miRNA reads from mouse generated on the MiSeq. So far I have trimmed adapters using Cutadapt and now... -
Not 100% mapping in output bam?
Running samtools flagstat on a bam file resulting from alignment with Hisat2 gives:
...Code:76075665 + 0 in total (QC-passed reads + QC-failed reads)
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HTSeq-count: Warning: x reads with missing mate encountered.
As I am running through an RNA-Seq pipeline using Hisat2 for alignment and HTSeq-count for counting reads in features I notice this warning at the bottom...Last edited by ronaldrcutler; 12-24-2016, 08:04 AM. -
Bowtie2 for miRNA-Seq
Hopefully someone can help. I have read conflicting info about aligners for miRNA data but I have finally decided on Bowtie2. I have 3 questions:
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Bash script to automate htseq-count
Hi everyone-
I am trying to write a script to automate htseq-count on a large number of samples. The script runs but then throws the following... -
Sorting SAM files
Hello all. I've been fiddling around with htseq-count using SAM files that were output by hisat2. I am using paired reads here and realized as I was going...Last edited by ronaldrcutler; 06-16-2016, 09:36 AM. -
Output count table in DESeq 2
Hello all,
I am trying to output the count table that is created to be used for differential expression analysis in DESeq. I'm just having... -
error with htseq count and bed tool
hello every one,
as i am working on count based differential analysis and for that i am trying to use HTSEQ and bedtools
1. I am... -
Does anyone know how cufflinks counts stranded data?
Hi,
I'm trying to make sense of the fpkm/coverage values produced by cufflinks. I have mapped paired-end stranded illumina data (fr-firststrand...
