11 results in 0.0022 seconds.
-
What exactly are "read groups"
I am reading the samtools manual. For the -r and -R flags in the view function, the manual refers to "read groups". I have not been able to... -
Samtools Depth
Hey Guys,
I have just installed samtools on the command line and am messing around with the features. One thing I am curious about is deletion... -
Summary: Troubleshooting for installing samtools in cygwin on Windows 07042014
Hi, All,
I am new user to samtools and Linux and in my short experience I found some people are asking same questions as I do, but answers... -
Pipelining "Samtools view" : invalid header in output .bam files
Hi,
I'm trying to filter properly paired and mapped reads from a BWA alignment using this command:
...Code:samtools view -hu -F4 bam_sorte
Last edited by fabfab; 04-02-2014, 12:25 AM. -
SamTools installation in Ubuntu
Hi
I am trying to compile SamTools on Ubuntu 13.01 ( dual boot on macbook pro). But when I am trying to run "make" its throwing me the... -
Using samtools view function in my own code?
Hey all,
I'd like to use samtools view function in my own code in order to map all the reads within some genomic coordinates such as chr1:200000-500000... -
Samtools multisample SNP caller
Hi -
I am running a comparison between running samtools SNP calling in the multi sample mode, vs using it on each file individually. I seem...Last edited by amcrisan; 11-06-2013, 03:56 PM. -
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:... -
Troubleshoot running coveragestats.py in Tablet (SamTools related)
I recently downloaded Tablet to assess read coverage of my de novo assembly of RNA-Seq of marine snail venom duct tissue. I have tried to run a script... -
creating .fai from .fa file using samtools faidx command
Hi everyone,
I am trying to create a FASTA index from a FASTA file using samtools:
./samtools faidx /home/krathi/data/ChIPseq/mm9/mm9.fa... -
TopHat2 run error
Hi All,
Whenever I run tophat2 it fails in the following section:
[2013-05-14 10:25:41] Mapping left_kept_reads to genome...
