Hello,
I have indexed my bam files as:
> samtools index -b file.bam
I get as a result a file.bam.bai. But when I try to convert it to BigWig with bamCoverage as:
> bamCoverage -b file.bam.bai -o file.bw
I get the following error:
[E::hts_hopen] fail to open file 'file.bam.bai'
[E::hts_open_format] fail to open file 'file.bam.bai'
The file file.bam.bai does not have BAM format
The error persists if I change the file name to file.bam.bai.
I checked with samtools flagstat, and I get the same error
> samtools flagstat file.bam.bai
[E::hts_hopen] fail to open file 'file.bam.bai'
[E::hts_open_format] fail to open file 'file.bam.bai'
samtools flagstat: Cannot open input file "file.bam.bai": Exec format error
If I dont index the bam file bamCoverage tells me i MUST index it first...
I think I have done this before without any problems and I dont understand why am I getting this error. Could it be that the files are corrupted? Any help is well appreciated!
1 answer
The .bai file is just an index, you have to convert the .bam file to bigWig - as shown on the bamCoverage documentation:
bamCoverage -b reads.bam -o coverage.bw
Hi, it seems like you don't have deeptools installed. Try,
bamCoverage --help
If this doesn't show you the help page, follow the deeptools installation instructions
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