RSeQC : infer_experiment.py Error: Could not retrieve index file
1
0
Entering edit mode
14 days ago
Prawesh • 0

I am trying to use RSeQC for identifying strandness but I am getting error as Could not retrieve index file

Code

infer_experiment.py --i test-sorted.bam -r output.bed12

Output:

[E::idx_find_and_load] Could not retrieve index file for 'test-sorted.bam'
Reading reference gene model output.bed12 ... Done
Loading SAM/BAM file ...  Total 200000 usable reads were sampled

Anyone knows how to address this issue?

RSeQC RNA-Seq • 246 views
ADD COMMENT
2
Entering edit mode
14 days ago
Trivas ★ 1.8k

You need to have indexed your bam/sam file using samtools index

ADD COMMENT
0
Entering edit mode

thanks, it's working now.

ADD REPLY
0
Entering edit mode

A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they all work. If an answer was not really helpful or did not work, provide detailed feedback so others know not to use that answer.

upvote_bookmark_accept

ADD REPLY

Login before adding your answer.

Traffic: 2712 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