Question: Error in running a Samtools mpileup script for getting base frequency information
0
gravatar for jigarnt
8 months ago by
jigarnt30
Canada
jigarnt30 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 • 442 views
ADD COMMENTlink modified 8 months ago by Devon Ryan64k • written 8 months ago by jigarnt30
2
gravatar for Devon Ryan
8 months ago by
Devon Ryan64k
Freiburg, Germany
Devon Ryan64k wrote:

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

ADD COMMENTlink written 8 months ago by Devon Ryan64k

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 REPLYlink written 8 months ago by jigarnt30

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

ADD REPLYlink written 8 months ago by Devon Ryan64k

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 REPLYlink written 8 months ago by jigarnt30
1

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

ADD REPLYlink written 8 months ago by Devon Ryan64k

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 REPLYlink written 8 months ago by jigarnt30

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

ADD REPLYlink written 8 months ago by Devon Ryan64k
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