How can I get gsnap to produce sam files with header? I am having difficulty with current dataset.

Hello, What is an appropriate loop for gmap gsnap alignment syntax for ~20K reference genomes? Essentially, I would like gmap gsnap to run through each …

Hey, I'm trying to preform a bisulfite alignment using gmapR package. This is my code: ========================= library("gmapR") ggd<-GmapGenomeDirectory(file.path(getwd(),"indices"), create=T) gg<-GmapGenome(file.path(getwd(),"test.fa"), directory=ggd, name="seq", create=T) cmet_index <- …

I want to use GMAP for my project, because Exonerate doesn't seem to be able to do multiprocessing/threading. I see the repo: https://github.com/juliangehring/GMAP-GSNAP has not …

Hello, I am not sure how to download the mm10 genome for genome guided alignment on GSNAP. In a separate project (for an Aiptasia alignment), …

Hi I tried to align almost more than 10 human genome datasets against the hg38. gsnap able to align, generating a truncated sam file. Can …

Hi I used gsnap (gmap-2014-12-24) to map my RNA-seq data. My PC has 16 Gig RAM and 8 core CPU. my used code was: ``` …

<p>Hi all, Has anyone align illumina paired end reads using BLAST, I used gsnap to do the alignment first, then use BLAST to align the …

<p>Is there anyway to get some kind of mapping score statistic from GMAP output? A score similar to e-value or mapping quality. It seems like …

Hi Everyone So I am working on rna seq data. I am using gsnap for my analysis(though I have also used tophat). With tophat , …