multicuv error Could not find indexes

Question

[PK]

I am trying to get new coordinated for my sequencing file so i tried to align my new version of the genomic file (TB927_v5.1). I used smalt to get sam file. I converted my sam file into bam file using this command:

samtools view -h -b -S out.sam > out.bam

Next, i used to multicuv

bedtools multicov -bams out.bam -bed merged.bed >nucleolus.txt

to get read counts but it shows

Could not find indexes

[Ram]

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Answer 1

[Nitin Narwade]

Have you indexed your bam file?

If not then just do it by using samtools utility.

Before doing an indexing you have to sort the bam file first.

Sorting Bam file:

samtools sort input.bam >sorted.output.bam

Indexing sorted Bam file:

samtools index sorted.output.bam

The second command will create bam file index in the same folder with .bai extension.

Now re-run the same command.