13 results in 0.0029 seconds.
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ErikTheNord started a topic error/mismatch rate threshold for long-read alignment with GMAP or minimap2in Generalerror/mismatch rate threshold for long-read alignment with GMAP or minimap2
Hello all -- my bioinformatics experience is mostly with mapping Illumina reads (to mammalian transcriptomes) using STAR. But lately my group is starting... -
What RNAseq mapper to use?
Hello everyone,
I am dealing with NGS data for the first time, so I am very new to everything. When I was looking for a read mapper for... -
GMAP-GSNAP Run Facing Issues
Hello All,
I am writing to understand if my installation of Gmap is accurate or not, since I am facing issues with its run. I have tested... -
extended cigar in gmap
Hi all,
I am aligning pacbio reads to a reference genome using gmap. Do you know how to output an extended CIGAR in output sam file from... -
The difference between gene loci with isoform in RNA-seq alternative anlalysis?
As I know, 'A locus (plural loci), in genetics, is the specific location or position of a gene, DNA sequence, on a chromosome. Gene loci analysis is generally... -
GMAP result with multi-mapping?
I have used GMAP to mapping my RNA-seq data to the reference genome with parameter ( -f samse -z sense_force -t 5 -n 0 --cross-species --allow-close-indels... -
How can I calcualte the sequence identity and coverage form GMAP output bam file?
Now I have got a bam file from gmap alignment with data from pacbio isoseq result. Now I want to get the statistic information about the coverage and...Last edited by huan; 01-20-2016, 12:37 AM. -
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.... -
GMAP problems: stopping at "Finished checking compiler assumptions"
Edit:
Never mind. It was a simple database error. Fixed it, but don't know how to delete post...
I am trying to map around 300 cDNA...Last edited by JonB; 04-28-2015, 08:03 AM. -
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... -
what is the gap column of GMAP output
Hello all--
Really simple, I hope simple to answer, question. What is the gap column in GMAP output? What do the codes mean? For example:... -
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,...
