RSeQC : infer_experiment.py Error: Could not retrieve index file

Question

[Prawesh]

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?

Answer 1

[Trivas]

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

[Prawesh]

thanks, it's working now.

[Ram]

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