Question

Data downloaded from GEO has raw transcript count matrix- can I still use tximport? Collapse raw transcript count matrix to GENE LEVEL

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agm • 0

@agm-21192

Last seen 4.5 years ago

Hello,

I have data as raw count matrix with ensembl transcript identifiers. I have successfully made a tx2gene table from a gtf file, but am stuck. I do not have individual files from Salmon or other transcript level packages which is the input for tximport.

Please help!!!!!!!!

tximport collapse • 746 views

ADD COMMENT • link updated 4.8 years ago by Michael Love 41k • written 4.8 years ago by agm • 0

score 1 · Answer 1 · 2019-07-03

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Michael Love 41k

@mikelove

Last seen 2 hours ago

United States

Hi,

I have to say, I don't really appreciate the exclamations. We provide support often after hours, as it’s not exactly effort that’s supported.

tximport only works for gene level summarization if you have also the counts, lengths and abundance (TPM).

ADD COMMENT • link 4.8 years ago Michael Love 41k

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Thank you! They were positive exclamations not negative ones- I completely understand the time constraint.

ADD REPLY • link 4.8 years ago agm • 0