This is a test version of Biostars. For the public version, visit https://www.biostars.org.
multicuv error Could not find indexes

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
rna-seq alignment software error
• 2,482 views • link
updated by Nitin Narwade Nitin Narwade • written by PK • PK

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

• 1 views • link
written by Ram Ram

1 answer

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.

• 1 views • link
written by Nitin Narwade Nitin Narwade

Log in to answer this question.

More posts like this