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gmap gsnap loop
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Question: Error in gmapR: gsnap not functioning
written by amer_ghl 0Hey, 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 <- …
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Where can I find GMAP? All links appear dead. Was the project abandoned?
written by mcsimenc 3I 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 …
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How to use GSNAP/GMAP for mm10 genome
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gSNAP aligner generating truncated sam file ?
written by pinn 21Hi I tried to align almost more than 10 human genome datasets against the hg38. gsnap able to align, generating a truncated sam file. Can …
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gsnap error (Unable to retrieve request for thread)
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Align Paired End Reads Using Blast
written by shl198 44<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 …
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Gmap Output Statistics
written by Damian Kao 1.6K<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 …
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How To Get Junctions File Using Gsnap
written by Varun Gupta 129Hi Everyone So I am working on rna seq data. I am using gsnap for my analysis(though I have also used tophat). With tophat , …