tximport from Galaxy output
1
0
Entering edit mode
@agustingonvi-20284
Last seen 24 months ago
Cleveland, OH

I am using Galaxy, and the output of both Salmon and Kallisto is an *.tabular file per sample with the following format:

Name Length EffectiveLength TPM NumReads ENSMUST00000193812.1|ENSMUSG00000102693.1|OTTMUSG00000049935.1|OTTMUST00000127109.1|4933401J01Rik-201|4933401J01Rik|1070|TEC| 1070 869.000 0.000000 0.000 ENSMUST00000082908.1|ENSMUSG00000064842.1|-|-|Gm26206-201|Gm26206|110|snRNA| 110 35.000 0.000000 0.000 ENSMUST00000162897.1|ENSMUSG00000051951.5|OTTMUSG00000026353.2|OTTMUST00000086625.1|Xkr4-203|Xkr4|4153|processed_transcript| 4153 3694.853 0.006244 0.926

Is it possible to input theses files into tximport? is so, how do I do that.

Thanks!

normalization tximport • 1.2k views
ADD COMMENT
1
Entering edit mode
@mikelove
Last seen 11 hours ago
United States

Yeah those are in Salmon format.

ADD COMMENT
0
Entering edit mode

Michael Love: which file of deseq2(salmon) we need to give as input to tximport and which gtf file.we.need to provide in usegalaxy?

ADD REPLY
0
Entering edit mode

See the tximport vignette, it explains all of this.

I can't provide support for Galaxy here.

ADD REPLY
0
Entering edit mode

Michael Love :Thank u

ADD REPLY

Login before adding your answer.

Traffic: 776 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6