Question

Combining RSEM Files with dif row # for tximport

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venura • 0

@venura-22066

Last seen 18 months ago

United States

Hi,

I have 4 .csv files containing gene level (transcripts collapsed) counts coming from infected (2 biological replicates) and non-infected (2 biological replicates) generated via RSEM. I dont have access to raw data files. Their contents are as follows;

gene_id transcript_id(s)    length  expected_count  FPKM
AT1G01010   AT1G01010.1 1688    88  2.68

However, number of rows in each file is different (My guess is 0 counts were removed). Can someone please help me by advising (or share a R script)me on how to get these data combined to match the input of tximport? so I can do the differential expression analysis using DESeq2. Thank you!

tximport DEseq2 RNAseq • 885 views

ADD COMMENT • link updated 5.3 years ago by Michael Love 43k • written 5.3 years ago by venura • 0

score 1 · Answer 1 · 2019-10-06

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Michael Love 43k

@mikelove

Last seen 1 day ago

United States

tximport is only for use on the original output files from the various software. You can obtain these or rerun the scripts for reproducibility sake. It’s not a safe idea to try to combine when you don’t know what’s missing.

ADD COMMENT • link 5.3 years ago Michael Love 43k

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Thank Michael! I agree. These data coming from an outside provider. They have provided RSEM output (.csv ). Their pipeline includes RSEM > DEseq2. I am trying to recreate their DESeq2 output (also provided as .csv). In a way this is me trying to see the reproducibility of their output. I appreciate if you can give me some guidance to achieve that.

ADD REPLY • link 5.3 years ago venura • 0

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I have no idea what they did. Presumably used estimated counts without an offset. Why not reach out to them for their scripts.