GMAP Output Cammand

Question

[Bioinfonext]

Hi,

I run gmap, by using this command:

/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

Answer 1

[WouterDeCoster]

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.

[EVR]

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

[Bioinfonext]

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.

[WouterDeCoster]

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.