Error in running a Samtools mpileup script for getting base frequency information

Question: Error in running a Samtools mpileup script for getting base frequency information

11 months ago by

Canada

jigarnt • 30 wrote:

Hi All,

I intend to know the base frequencies at each positions in my BAM files. For the same, I am using samtools mpileup script, which can serve the purpose. While running the script, I am encountering an error which is not understandable by me. So I am reaching out to all the expert bioinformaticians for their assistance. I have posted the error below for your reference:

/Users/Desktop/Tools/samtools-1.3/samtools mpileup -f GCF_000184105.1_Geom_destructans_V1_genomic.fa -r supercont1.1-supercont1.1847 712206_realigned_reads.bam N_american_realigned_reads.bam Nova_Scotia_1_realigned_reads.bam

[E::mpileup] fail to parse region 'supercont1.1-supercont1.1847' with 712206_realigned_reads.bam

Thank you in advance.

mpileup genome • 538 views

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modified 11 months ago by Devon Ryan ♦ 68k • written 11 months ago by jigarnt • 30

11 months ago by

Devon Ryan ♦ 68k

Freiburg, Germany

Devon Ryan ♦ 68k wrote:

supercont1.1-supercont1.1847 isn't a meaningful region designation. I assume you mean something like supercont1.1:1-1000.

ADD COMMENT • link written 11 months ago by Devon Ryan ♦ 68k

Hi Devon,

Thank you for your response. I tried your suggestion of indicating the chromosome positions but it is giving me the same error:

/Users/lindakohn/Desktop/Tools/samtools-1.3/samtools mpileup -f GCF_000184105.1_Geom_destructans_V1_genomic.fa -r supercont1.1:1-1847 712206_realigned_reads.bam N_american_realigned_reads.bam Nova_Scotia_1_realigned_reads.bam

[E::mpileup] fail to parse region 'supercont1.1:1-1847' with 712206_realigned_reads.bam

Also, I want to add that my Reference Fasta is composed of 1847 contigs and they are described as: Supercont1.1 to Supercont1.1847. In that case, can there be any other errors?

ADD REPLY • link written 11 months ago by jigarnt • 30

If the contig is called Supercont1.1 in the fasta file, then you need to type that instead of supercont1.1.

ADD REPLY • link written 11 months ago by Devon Ryan ♦ 68k

Hi Devon,

In the file, it is actually supercont1.1. and not Supercont1.1. Would you mind having a look at the fasta file? It is available at the NCBI. It is an 30mb file so would not consume much time of yours. Organisms name is Geomyces destructans

ADD REPLY • link written 11 months ago by jigarnt • 30

In my copy (here) the contigs are named NW_012234580.1 and NW_012234581.1 and so on.

ADD REPLY • link written 11 months ago by Devon Ryan ♦ 68k

Hi Devon,

Many thanks for having a look at it. I tried with those numbers before, but got the same error. Is there any other way, to get the base pair information at each positions in your BAM files?

ADD REPLY • link written 11 months ago by jigarnt • 30

Please post your BAM file somewhere and I'll have a look.

ADD REPLY • link written 11 months ago by Devon Ryan ♦ 68k

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