I am doing an RNA-seq analysis where I have used featureCounts to count the number of reads per gene feature. The output looks like this:
...
55 results in 0.0025 seconds.
-
featureCounts output to DESeq2?
-
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... -
Problem with UCSC GTF files?
Hi,
I would like to ask for some opinion and advice related to the different available GTF-file sources for annotated genes.(mm10, but... -
Problem with UCSC GTF files??
Hi,
I would like to ask for some opinion and advice related to the different available GTF-file sources for annotated genes.(mm10, but... -
RefseqGene vs Ensembl for mm9
Hello,
I would like to ask for your opinion regarding a reference transcriptome for mm9. My task is to search for "novel" transcripts... -
dexseq_prepare script error with Ensembl human gtf
Hi all
I was following the instructions to analyze my RNASeq data with the DEXSeq package but I run into the following error while preparing... -
How to decide the side (5' or 3') close to TSS in GTF
Hi everybody
I’d like to ask you about TSS (transcription start site) annotation
Now I’m analyzing Total RNA-seq data by ENCODE... -
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... -
Tophat transcriptome indexing
Hi,
I'm trying to use tophat on some data and am having an issue. I want to make a transcriptome mapping file like this:
... -
tophat2/2.1.0 error running from bam2fastx
I am running tophat2.1.0 (bowtie 2.2.6.0) on SE RNAseq data and encountering the following error:
[2016-02-29 09:38:34] Beginning... -
Something wrong in FlyBase's gtf (gff to gtf conversion)
Hi All,
I wanted to re-create FlyBase's gtf (FB2015_04) from the gff file. It is a different matter why I want to do that.
... -
I Have Variants and positions and need to make a GTF file. Help
Hi,
I'm very new to this and I'm working on my first project. I have a list of Variants and their location. I have been tasked with creating...Last edited by JdevSEQnoob; 09-25-2015, 03:34 AM. -
Reference annotation file (gtf) for the NOD/ShiltJ mouse?
Hi,
I am in desperately looking for a reference annotation file (gtf) for the NOD/ShiltJ mouse so that I may run Cuffmerge.
... -
Problems with cufflinks GTF annotated files and DEXSeq
I'm trying to use a Cufflinks GTF that includes novel isoforms as an input for DEXSeq.
My RNA-Sseq libraries were stranded and my cufflinks command... -
Tophat error with Cuffmerged GTF
I'm trying to run Tophat 2.0.13 (bowtie 1.1.1) on colorspace csfasta and qual files using a GTF produced by Cuffmerge (Cufflinks 2.2.1) as a -G option....
