Dear all ,
I tried to use eXpress to count the mapping results obtained with Bowtie2.
The command used is
express -m 450...
17 results in 0.0030 seconds.
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Bug with eXpress: Unable to open input SAM file
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samtools mpileup possible bug
Hello,
I noticed that last sample (last 3 columns) in mpileup format behave strangely in positions with low base quality (< 13). It looks... -
BCFtools will not filter fixed sites
Hello all,
I'm encountering a surprising problem while filtering a vcf file in bcftools (v1.1-52-ga2e5b56). It doesn't look like a proper... -
Linux Mint: Not playing nice with bioconductor/edgeR. Why?
I am running Linux Mint (a variant of Ubuntu basically). I get the following warning messages:
...Code:> source("http://bioconductor.org/biocLite.R") -
Possible picard bug
Hey, I am running picard to remove pcr-duplicates using MarkDuplicates.jar
on bam file porduce by tophat(with fusion-serach on), and I encount:... -
Asymmetric trimmomatic output with paired-end RNA seq. data
I have data from two experiments of 6 samples each that used 2x100 b paired-end Illumina HiSeq 2000 RNA sequencing with unstranded libraries in case of... -
duplicate tags tophat2
I am using tophat2 (2.0.10) with bowtie2 to map Illumina HiSeq 2000 2x100 paired-end RNA sequencing data to the human genome/transcriptome.
... -
Novoalign inappropriately softclipping?
I have downloaded some exome data that appears to have been aligned using Novoalign
I determined this from the header:
@PG ID:novoalign... -
Bug/Feature in Tabix?
I had posted this report on BioStars, http://www.biostars.org/p/68757/, regarding what I consider to be a bug in Tabix. If I query a single position in... -
Possible tophat 2.0.6 bug?
Hi all,
I am trying to use tophat to map SOLiD colorspace pair-end (50x35) reads with tophat. However, when I tried with the standard procedure... -
Possible samtools view bug
I'm using samtools to extract some regions from a BAM file, and in some situations, I don't get back all of the reads that overlap the region.
... -
Is it a bug in BWA?
After finishing BWA alignment, the result displays a strange phenomenon. That is a read whose flag showed it is unmapped read however ending with specific... -
Can't add sff files in gsAssembler and gsMapper v2.7
Hi,
I have managed to install version 2.7 of the roche assembler and mapper on ubuntu 12.04 but I am left with a weird problem.
... -
Cufflinks gets stuck at chrUm fron (rat) rn4 mapping
Dear all,
I do not mean to cross post, but maybe starting a new thread will help to solve this issue.
I read some posts from Bioinformatics... -
An important bug in BLAST+ 2.2.26+
Hi everyone,
TL;DR: Always use the -max_target_seqs flag when using BLAST unless you are using default verbose output, otherwise you might...
