Transcript ID partially converted to genId

[ramay]

Hi,
Thanks for making this webtool and keeping it upto date! I had run a dataset with iDEP about two years ago and everything went well as I expected. This week I was trying to re-run the data on the webtool and I am finding a weird error in the deseq results.

Only a few of the transcript ids are being changed to gene ids and the rest of the DEG list has transcript id but no gene name. here are the first few rows form the files. The rest of the rows are transcript ids only. Can you please help me figure out what is going on.

Thanks!
Hena

Row-names	Symbol	HA107-GF___log2FoldChange	HA107-GF___padj
ENSMUSG00000064341	mt-Nd1	-0.3247938	0.60009087
ENSMUSG00000064345	mt-Nd2	-0.1708228	0.77349927
ENSMUSG00000064351	mt-Co1	-0.1339647	0.80554946
ENSMUSG00000064354	mt-Co2	-0.4221777	0.51625553
ENSMUSG00000064356	mt-Atp8	-0.0757906	0.88785179
ENSMUSG00000064357	mt-Atp6	-0.3694733	0.5005814
ENSMUSG00000064358	mt-Co3	-0.3744667	0.51403268
ENSMUSG00000064360	mt-Nd3	-0.7747606	0.35351245
ENSMUSG00000064363	mt-Nd4	-0.1271418	0.81377119
ENSMUSG00000064367	mt-Nd5	0.14233175	0.77107721
ENSMUSG00000064368	mt-Nd6	-0.3473448	0.61255174
ENSMUSG00000064370	mt-Cytb	-0.192405	0.72193194
ENSMUSG00000065947	mt-Nd4l	0.16466402	0.70428999
ENSMUST00000000001.4	NA	-0.3471355	0.09450685
ENSMUST00000000010.8	NA	4.04451566	0.07043839
ENSMUST00000000028.13	NA	1.11132184	0.31293435
ENSMUST00000000033.11	NA	-0.3380975	0.65479814
ENSMUST00000000049.5	NA	0.65922943	0.46285746
ENSMUST00000000058.6	NA	0.56286036	0.48210573
ENSMUST00000000080.7	NA	-1.244181	0.008549
ENSMUST00000000087.12	NA	0.46693129	0.36588882
ENSMUST00000000090.7	NA	-0.3303867	0.50338515

[gexijin]

Thanks for sending us feedback. This might be caused by recent changes in iDEP. Originally, we converted
ENSMUST00000000087.12 as ENSMUST00000000087, automatically, then these transcript ids are converted to gene IDs.
Recently we found that this made it impossible for some gene IDs in some species. So we removed this.

To make it work, I suggest that you convert your transcript IDs first in Excel, then upload to iDEP.