Question: GMAP Output Cammand
0
gravatar for Bioinfonext
3.5 years ago by
Bioinfonext220
Korea
Bioinfonext220 wrote:

Hi,

I run gmap, by using this cammand:

/home/yog/software/gmap-2016-11-07/src/gmap -D /home/yog/database -d genome Trinity.fasta -f samse

but how can I store gmap result in a output folder.

Thanks

rna-seq tool • 2.9k views
ADD COMMENTlink modified 3.5 years ago by WouterDeCoster43k • written 3.5 years ago by Bioinfonext220
2
gravatar for WouterDeCoster
3.5 years ago by
Belgium
WouterDeCoster43k wrote:

I assume the output is printed to the terminal? In that case, you need to redirect the result to a file, e.g.:

gmap -D /home/yog/database -d genome Trinity.fasta -f samse > youroutput.sam

Furthermore, it's probably advisable to follow a (Linux) command line tutorial.

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by WouterDeCoster43k
1

@WouterDeCoster rightly said. @Nabiyogesh must read basic linux commands first before he uses any bioinformatics tools

ADD REPLYlink written 3.5 years ago by EVR570

Thanks

Can you please suggest how I can get mapping statistics: How many of the transcripts were mapped to draft genome and also the transcript ID list which do not show mapping to draft genome.

ADD REPLYlink written 3.5 years ago by Bioinfonext220

I think it's time that you start fixing things yourself without turning to us for helping you every time you encounter something new. None of us was born with "bioinformatic skills", every single one of us learned it through struggling and solving things.

We are volunteers and are happy to help everyone, but we are not supposed to do your entire project step by step.

ADD REPLYlink written 3.5 years ago by WouterDeCoster43k
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