Question

tximport from Galaxy output

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agustin.gonvi ▴ 20

@agustingonvi-20284

Last seen 2.7 years 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 • 1.5k views

ADD COMMENT • link updated 3.1 years ago by Pragathi • 0 • written 5.5 years ago by agustin.gonvi ▴ 20

score 1 · Answer 1 · 2019-06-21

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Michael Love 43k

@mikelove

Last seen 4 days ago

United States

Yeah those are in Salmon format.

ADD COMMENT • link 5.5 years ago Michael Love 43k

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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 • link 3.1 years ago Pragathi • 0

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See the tximport vignette, it explains all of this.

I can't provide support for Galaxy here.

ADD REPLY • link 3.1 years ago Michael Love 43k

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Michael Love :Thank u

ADD REPLY • link 3.1 years ago Pragathi • 0