GMAP: a genomic mapping and alignment program for mRNA and EST sequences

Question

[Bioinfonext]

Deal all,

I installed GMAP, and build indexing of draft genome using gmap_build by using this cammand.

/home/yog/software/gmap-2016-11-07/util/gmap_build -D /home/yog/database/ -d custard_genome Custard_1.0.chromosomes.fix.fasta

Now want to align trinity assembled transcript to genome.

my aim is to extract those de novo assembled trinity transcripts that do not able to map on draft genome.

Please suggest how I can do by using GMAP and also share cammand lines.

Thanks Yogesh

[WouterDeCoster]

Please use a more informative question for your question. In addition, it's good practice to show us what you tried. You should also start with reading the manual.

[devnbfgr13]

I am aligning a fastq bacteria reads to my transcriptome assembly using Bowtie2, And shorted the Sam to BAM. The mapped reads file has only one sequence while the bam file has 4.5 Gb data. How it is possible.

Thanks in advance. DEV

[WouterDeCoster]

I don't see a link between your question and the original question here. Please open a separate thread for your issue and be as informative as possible, including all commands you used.

Answer 1

[EVR]

Hi Yogesh,

Once you try to map the de novo assembled transcriptome onto genome, in the console file, it will list out the transcripts which cannot be aligned tin the genome. You can make use of those transcripts for your analysis. Command:

gmap -D /path/to print/your/output -d path/of/your/built/GMAP_DB/ trinity.fasta

Also consider the options like coverage, identity, chimeric_alignments etc, if needed

[Bioinfonext]

Hi Thamizh

Thank you very much for reply.

When I do Is to gmap installation folder it shows following files...

gmap-2016-11-07]# ls acinclude.m4 AUTHORS config config.site configure COPYING libtool Makefile.am NEWS README tests util aclocal.m4 ChangeLog config.log config.status configure.ac INSTALL Makefile Makefile.in NOTICE src TODO VERSION

Can you suggest me where is the script to run gmap for mapping transcript sequences to genome, for genome indexing script was in util but mapping I am not sure which one I should use..

Thanks Yogesh

Answer 2

[Bioinfonext]

Dear All,

When I do Is linux cammand to gmap installation folder it shows following files...

gmap-2016-11-07]# ls acinclude.m4 AUTHORS config config.site configure COPYING libtool Makefile.am NEWS README tests util aclocal.m4 ChangeLog config.log config.status configure.ac INSTALL Makefile Makefile.in NOTICE src TODO VERSION

Can you suggest me where is the script to run gmap for mapping transcript sequences to genome, for genome indexing script was in util but mapping I am not sure which one I should use

Thanks Yogesh

Answer 3

[Bioinfonext]

Dear All,

When I do Is linux cammand to gmap installation folder it shows following files...

gmap-2016-11-07]# ls acinclude.m4 AUTHORS config config.site configure COPYING libtool Makefile.am NEWS README tests util aclocal.m4 ChangeLog config.log config.status configure.ac INSTALL Makefile Makefile.in NOTICE src TODO VERSION

Can you suggest me where is the script to run gmap for mapping transcript sequences to genome, for genome indexing script was in util but mapping I am not sure which one I should use

Thanks Yogesh

Answer 4

[Bioinfonext]

Dear All,

Thanks, it is resolve.

Yogesh

Answer 5

[Bioinfonext]

Hi,

I run gmap, by using this cammand:

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

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

Thanks Yogesh

[EVR]

/home/yog/software/gmap-2016-11-07/src/gmap -D /home/yog/database -d radish_genome Trinity.fasta -f samse >output.gff3 2>log,txt

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