Is there really no way (program, tool) to tell if your BAM files have amplicon reads?
How is everyone doing it? determining a priori and...
18 results in 0.0098 seconds.
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Find out if you have amplicon reads.
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BWA not outputting sequences
Hi, I am having an issue with BWA genome alignment where sequence information is not being stored (i.e. sequence output in bam file is a * ). Can anyone... -
TCGA RNAseq BAM Files
Hi
My PI is interested in acquiring BAM files of RNAseq of breast cancer/cancer tumor/cell lines. I know TCGA may have them, how can we... -
Sorted BAM read count >2x total FASTQ count
This might be a silly question but it is bugging me and I need the answer. I have a set of paired end FASTQ files that contain about 30 million reads... -
Stand alone torrent variant caller -g request
Hi!
I am trying to run the stand alone torrent variant caller on an 18-month old BAM file that was aligned to some version of hg19
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the "chr" in the chromosome name
Hi,
I have been given a few exome datasets (already mapped and I don't have the fastq files). The problem is that when these were mapped, they... -
how do i create an rg.txt file for input into samtools merge? / picard
Hi,
I have merged bam files from 6 lanes for a number of samples, and am trying to use picard MarkDuplicates. However, I get an error PicardException:... -
Smatools mpileup thinks my sorted bam files are not sorted
Hi
I am trying to run samtools mpileup on a large list of bam files
...Code:samtools mpileup -d 5000 -f /path/to/ref.fa \ /path/to/first.bam
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Samtools view -c Readcount Issue
I'm using samtools to determine the total number of reads in a uniquely large bam file as shown below. I'm having a hard time interpreting the result.... -
Basic data extraction on bam files
I'm trying to get read counts for things like reference normal forward/reverse count, alternative/reference forward/reverse counts from a bam file. I've... -
Downloading all CSHL long RNA seq data from UCSC FTP server
Hello there,
I'm trying to download all the bam & bam.bai files of ENCODE's CSHL long RNA seq data for a particular genomic locus using...Last edited by superfly; 01-03-2013, 05:18 AM. -
Problem with samtools depth?
I'm trying to plot the depth of coverage but when running samtools depth it seems to skip over bases which I presume have no alignments spanning those... -
Extracting reads from BAM files
Hi All,
I am new to samtools and some help will be awesome.
I have BAM files and I have a long list of loci which I want... -
sorting bam files
Hi,
I have run a bowtie followed by a tophat with the unmapped reads.
I than want to merge the two sam files (output).... -
Truncated BAM files from 1000GP
I got this error message from SAMTOOLS:
samtools view -q 30 NA12878.chrom1.SLX.maq.SRP000032.2009_07.bam 1:532036-533055
[bam_header_read]...
