Hi everybody,
For my RNA-seq analysis, I wanted to use GSNAP to align my reads.
Building the index ran without any problems, but...
12 results in 0.0029 seconds.
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GSNAP error Problem Sequence
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GSNAP: align_score higher than set in -m
Hi All,
I'd like to clarify something which I find odd on my GSNAP output.
I ran GSNAP (version 2015-09-29) like this (i.e.... -
GSNAP: (too many?) mismatches in -N mode
I've just tried running GSNAP version 2014-12-29 to predict novel splice junctions using -N. My input files are paired-end fast files, 75t.
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gmap_build error
Hi guys,
I am in process of configuring GSNAP on the cluster of my university however I am repeatedly encountering an error in one step and I cant...Last edited by Satya; 07-15-2014, 11:42 AM. -
GSNAP output to IGV
I aligned Illumina reads to the zebrafish v9 reference genome using GSNAP. I had to build a new genome database in GSNAP/GMAP from individual fastA files... -
gsnap: How to output only alignments with minimal number of mismatches?
Hi there,
I am aligning paired-end ChIP-Seq data of drosophila transcription factors.
I would like to have a .sam file with... -
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. -
Tophat/GSNAP: proper-paired reads
Hi Everyone,
I tried Tophat v 2.0.6 and GSNAP v 2013-02-05 to align Illumina paired-end reads. However, the numbers of proper-paired reads...Last edited by riziai; 04-26-2013, 12:40 PM. -
Tophat + Cufflinks vs. CLC Bio
Dear all,
I'm currently analysing RNAseq data (Illumina paired end, read length 101 bases) in order to investigate different cancer stages.... -
Cufflinks models from gsnap alignments extend beyond the reference
I'm using Cufflinks 2.0.0 without a reference GTF to build models from GSNAP v20120427 alignments, also made without a reference GTF (i.e. using -N 1).... -
GMAP vs GSNAP
Hello all,
I was wondering if someone could enlighten me as to the difference between GMAP and GSNAP, their advantages and disadvantages,... -
GSNAP Output splice junctions
Matter resolved, thread can be closed.Last edited by ChrisAU; 01-26-2012, 04:05 AM.
