Question: Combining RSEM Files with dif row # for tximport
0
gravatar for venura
6 weeks ago by
venura0
venura0 wrote:

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!

rnaseq deseq2 tximport • 81 views
ADD COMMENTlink modified 6 weeks ago by Michael Love26k • written 6 weeks ago by venura0
Answer: Combining RSEM Files with dif row # for tximport
1
gravatar for Michael Love
6 weeks ago by
Michael Love26k
United States
Michael Love26k wrote:

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 COMMENTlink written 6 weeks ago by Michael Love26k

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 REPLYlink written 6 weeks ago by venura0
1

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

ADD REPLYlink written 6 weeks ago by Michael Love26k

Thank you. I will do that.

ADD REPLYlink written 6 weeks ago by venura0
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