Question

what the first row without a gene name?

1

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Raymond ▴ 20

@raymond-14020

Last seen 5.5 years ago

Hi, all,

I aligned my RNAseq raw data to cDNA using Kallisto and import the result using tximport as suggested by the DESeq2 tutorial (tx2gene maps ensembl_transcript_id to ext_gene symbol)

txi.kallisto_gene <- tximport(files, type = "kallisto", tx2gene=tx2gene,ignoreTxVersion=TRUE)

When I looked into the txi.kallisto_gene, it shows as below, the first row does not have a name, anyone knows how to deal with it? can I just ignore it?

               495-RB-139   495-RB-140   495-RB-141 495-RB-142  495-RB-143 495-RB-144
              84021.18351 102743.98948 151863.14971 97510.1275 78587.59879 87162.3374
0610009B22Rik   494.00005    606.99973    405.99960   692.9998   493.99982   564.0001
0610009O20Rik  1043.00000   1466.00000    806.00000  1172.0000   947.00000  1325.0000
0610010F05Rik  1571.00019   2090.99933   1227.99979  1779.0010  1632.00373  1772.0035

deseq2 • 1.4k views

ADD COMMENT • link updated 3.9 years ago by James W. MacDonald 67k • written 6.9 years ago by Raymond ▴ 20

score 1 · Answer 1 · 2018-01-26

1

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Michael Love 43k

@mikelove

Last seen 7 days ago

United States

This occurs because you have transcripts associated with the empty string in your tx2gene table. Take a look at that table and you can solve the problem there one of two ways, either giving them the transcript ID as a gene ID, or removing those transcripts from the table. I don’t know which way to go is better.

ADD COMMENT • link 6.9 years ago Michael Love 43k

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Thanks Michael. I tried the first way, giving them the paste0("UNKNOWN",transcriptID) as the gene ID.

ADD REPLY • link 6.9 years ago Raymond ▴ 20

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Hi Raymond. Could you please elaborate on where exactly you inserted the paste0 code into the tximport script? I'm having the exact same problem as you right now.

ADD REPLY • link 3.9 years ago anand.gururajan ▴ 10

0

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Please don't reply to years-old posts. Instead, post a new question, and if you want to reference the old post, just insert a hyperlink to it (copy the URL, then hit the globe with a green arrow above the box you are typing in, and paste in the link to the old post).

ADD REPLY • link 3.9 years ago James W. MacDonald 67k