No. All of the positions in the pileup file are N's and my reference sequences do not consist of all N's.
Sarah
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my command:
samtools pileup -f myref.fas my_sorted_assembly.bam -c > mydata.pileup
my output (e.g.):
NT_033777 27895205 N A 24 0 6 17 aaaaaaaaaaaaaaaaa $))))))()')))")))
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Originally posted by nilshomer View PostPost the command you are using so we can help
Did you specify the FASTA file with the "-f" option?
command:
samtools pileup -f reference.fa sorted.bam > raw.txt
output (e.g.):
chr7:150849-150991 22 N 2 GG CC
Renee
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Originally posted by skingan View PostHello,
I am using samtools to generate a pileup file from a Mosaik genome assembly. My problem is that the pileup file contains all "N's" in the reference sequence field (column 3). I have double checked that I am using the exact same multi-sequence fasta file as the reference for both Mosaik and samtools.
Has anyone ever run into this before? I am using MosaikSort and MosaikText to generate a sorted bam file for input into samtools. Without the reference, I cannot get SNP quality scores, which is the whole point of my analysis.
Thanks for your help,
Sarah
[email protected]
Originally posted by reneeg36 View PostHi,
I am having the same problem. I am mapping reads to a list of contigs from a de novo assembly using bwa. I have converted the bwa sam alignment file to a sorted bam file using samtools. When I try running pileup to identify variants, I get only N's in the reference base position. I have checked the reference fasta file and don't find anything wrong.
Thanks!
Renee
[email protected]
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Hi,
I am having the same problem. I am mapping reads to a list of contigs from a de novo assembly using bwa. I have converted the bwa sam alignment file to a sorted bam file using samtools. When I try running pileup to identify variants, I get only N's in the reference base position. I have checked the reference fasta file and don't find anything wrong.
Thanks!
Renee
[email protected]
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samtools problems with reference in pileup file
Hello,
I am using samtools to generate a pileup file from a Mosaik genome assembly. My problem is that the pileup file contains all "N's" in the reference sequence field (column 3). I have double checked that I am using the exact same multi-sequence fasta file as the reference for both Mosaik and samtools.
Has anyone ever run into this before? I am using MosaikSort and MosaikText to generate a sorted bam file for input into samtools. Without the reference, I cannot get SNP quality scores, which is the whole point of my analysis.
Thanks for your help,
Sarah
[email protected]
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