55 results in 0.0039 seconds.
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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... -
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 - how do I cimport it for Cython?
TL;DR
How do I `cimport HTSeq` in Cython module?
--- Details ---
I am trying to use HTSeq to read BAM files that are quite large...Last edited by Proteos; 03-26-2018, 01:28 PM. -
How to create a GTF/GFF file for HTSeq OR how to count reads without GTF?
I am working with RNAseq of an insect under different treatments. I already have the data (Illumina HiSeq paired-end reads) and I was planning to follow... -
Overlapping 5UTR-CDS features with HTSeq: Ambiguous?
My colleagues and I are interested in the distribution of reads that fall within the 5'UTR, CDS and 3'UTR of a given transcript. We made a feature count... -
hisat2 file reads don't match up
Hello all. For a few of my samples, I am getting this error that the reads aren't matching up between my two mates:
...Code:Error, fewer reads in file
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Tab delimited text files of gene counts
Hello all. I have merged .bam files containing count reads for each gene for each sample (biological replicate). I would get a tab delimited text file... -
HTSeq - NameError: name 're' is not defined
I'm trying to use HTSeq but getting "NameError: name 're' is not defined" after import HTSeq command. As I'm a novice, I don't know how to resolve... -
HTSeq_output_Error_occured_when_processing_SAM_input
Dear, SEQanswers community,
I faced issue with creation counting tables for RNA-seq data using HTSeq software.
Before I performed... -
HTSeq-qa question
Hi guys,
I was just wondering if there is any trick on using htseq-qa on multiple files? i have around 50 fastq files, and it can be time... -
question about RNA-Seq and strandness information
Hi,
I'm fairly new to RNA-Seq data analysis and I'm a bit confused about something and I'd like to get your views on it. I have run an RNA-Seq... -
Error using HTSeq
Hi,
I am relatively new to using Linux and to RNA-seq data analysis. I have been given some BAM files and been told to analyse the data... -
Understanding edgeR protocol from Anders et al 2013
Hello, I am using edgeR for the first time, and relying on the edgeR user's guide and Anders et al 2013 protocol in Nature Protocols to help me along.... -
DESeq2 depends on GeneOrder?
Dear all,
currently we are thinking about replacing HTseq count by featureCount from the Subread package. The run time is shortened considerably,... -
Using HTSeq-count when no attributes are available?
I have been using htseq-count with great success, except for one particular type of genome feature, the transposable elements (te).
There is no...
