51 results in 0.0033 seconds.
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BBMap pileup questions
I am interested in metrics that summarise coverage from my BAM file. I came across BBMap pileup which does a decent job. But I have a couple of questions.... -
BBMap pileup questions
I am interested in metrics that summarise coverage from my BAM file. I came across BBMap pileup which does a decent job. But I have a couple of questions.... -
Pileup file: base positions on reads
Why are there more base positions than nucleotide reads in a samtools pileup file generated using the -O argument (output base positions on reads)? I... -
SRA data in pileup format
Hello all,
I'm trying to use the first pileup file the below link points to:
http://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SR... -
Error: Invalid format for pileup at line null in varscan2
Hi,
I am using Varscan2 with readcounts like follows
...Code:samtools mpileup -f /home/tsekara/Transcriptomes/trinity5_frameDPcorrected.fa
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generating pileup of paired end fragments
Dear all,
i'm working with paired end rnaseq data. i wanted to generate a pileup with samtools mpileup but noticed that only the mapping reads get...Last edited by Slacanch; 01-20-2015, 08:42 AM. -
Pileup differences with different SAMtools versions
Hello,
Generating pileups of bacterial data sets with SAMtools 0.1.18 and 0.1.19, I have noticed differences in the pileup files. Version... -
Bio-SamTools pileup method
Hello
Im trying to use Bio:: DB::Sam to get list of reads covering certain position .Sam file using pileup method using this code
...Code:use strict;
Last edited by m4merg; 07-31-2014, 08:19 AM. -
Convert pileup to bed
Hello,
I'm currently using samtools mpileup like this:
...Code:samtools mpileup -l target_regions.bed file1.bam file2.bam file3.bam
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Samtools mpileup - start and end segments
Hi,
I'm having a problem calling a variant with NGS which has been confirmed via Sanger sequencing.
I'm using samtools mpileup... -
loss of bases using mpileup
I have noticed a problem with mpileup (samtools) that results in a large loss of reads for certain base positions, with some bases being entirely absent.... -
Coverage tables for samples
Hello everyone,
I am generating coverage tables (tables containing the coverage for each base in the reference genome), and I found 2 ways... -
Slow Pileup After Switching to Stampy
I'm calling the pileup like this:
I used to use BWA to generate...Code:samtools pileup -f ref.fa aln_reads.bam -c > out.pileup
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Indel analysis (SAMtools:pileup or mpileup)
Hi! I am doing indel analysis, using SAMtools/bcftools. First I tried to use mpileup with the command line:
samtools mpileup file.fa file.bam... -
samtools pileup manual description
Hello all,
I am trying to use a shell script that calls samtools pileup function. Because the pileup function is deprecated, the shell...
