biomaRt correct annotation but...
1
0
Entering edit mode
7.1 years ago
Mozart ▴ 330

Hi everyone, I am a bit confused about a painful step of my pipeline using Sleuth. I am trying to move from the transcript level to the gene level and that's why I am using biomaRt. PS: please pardon my ignorance in term of bioinformatic jargon

RNA-Seq • 2.1k views
ADD COMMENT
3
Entering edit mode
7.1 years ago

Hey there,

Do you get results after running a test?

Basically, there is some weirdness between some of the ensembl annotations. Your transcriptome probably says something like 'ENSMUST00000148678.2' for that specific transcript. When we try to merge that with the target_mapping, it ends up being empty because the target_id is 'ENSMUST00000148678' (note the missing .2). It's basically just telling you that we removed .N and it seems to have fixed it. When we do that and there is no intersection mapping still, then the program will completely error.

If you still get results after running a test and calling sleuth_results(), then everything should be fine.

Best,

Harold

ADD COMMENT
0
Entering edit mode

Thanks a lot Harold, actually everything should be fine even if I am getting the error.

ADD REPLY

Login before adding your answer.

Traffic: 1049 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6