59 results in 0.0023 seconds.
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Paired-ends data aligning preferentially to specific strands
I have some PE bs-seq data which is aligning very strangely: the left reads are aligning only to the - strand and the right reads only to the + strand.... -
Problem with Bowtie 2
Hi, I am a student and I'm doing work with data obtained by ChiPSeq. I am trying to do the alignment of the reads with the reference genome, but I get... -
Problem with Bowtie 2
Hi, I am a student and I'm doing work with data obtained by ChiPSeq. I am trying to do the alignment of the reads with the reference genome, but I get... -
Really Low Bowtie2 Alignment Numbers From Demultiplex in STACKS
In STACKS, I ran process_radtags and get close to 20 million reads. They are paired-end 150bp reads.
/home/srile14/stacks-1.48/process_radtags... -
Scalpel indel caller running slowly on TCGA WGS BAM files
Hi members,
I am trying to use the Scalpel indel caller (http://scalpel.sourceforge.net/) to find indels in WGS files from TCGA. But am... -
hisat2 file reads don't match up
Hello all. For a few of my samples, I am getting this error that the reads aren't matching up between my two mates:
...Code:Error, fewer reads in file
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hisat2 multiple thread usage
Hello all, I am trying to switch over to using hisat2 instead of tophat. I have a couple questions:
1. It seems that we are able to input... -
mutationalMeltdown started a topic Assigning taxonomy to shotgun metagenomic reads: sequence alignment or composition?in MetagenomicsAssigning taxonomy to shotgun metagenomic reads: sequence alignment or composition?
I'm interested in identifying bacterial pathogens from shotgun metagenomic data. Crudely, I envisage the pipeline to be something like this:
1)... -
how use bowtie2 output sam file for magan5 input
I'm new to bioinformatics and I need to know how can I use bowtie2 output .sam file to megan5 to view polytechnic tree of microbes.I use Silva DB as reference... -
Bowtie2-Samtools. Too many degenerated bases
Hi all,
this is my first-question message in the forum, so I hope it's in the right place. I've had a look to related threads with a similar... -
Bowtie - seaching for less aligned reads
Hello,
I'm trying to use BOWTIE to find less aligned sequences to the mouse genome, and even better sequence that has 0 % matching....Last edited by Nastya; 08-30-2015, 11:47 PM. -
bowtie2-align dided with the signal 11 (SEGV) (core dumped) with bowtie2
I am running bowtie2 to map 300 bp reads to a fixed set of amplicons.
I always get a "bowtie2-align died with the signal 11 (SEGV) (core... -
bowtie with humongous reference database
Hi all,
I have been trying to find a way to build bowtie2 index for a really large reference database (>100GB) but I keep running into... -
views Bowtie2 : aligned result read count not matching with sam Read count
bowtie2 -f -N 1 -p 8 -x REF.fa -1 sample01_1.fasta -2 sample01_2.fasta -S sample01.sam --al sample01_al.fasta --al-conc sample01_alcon.fasta
...Last edited by vinumanikandan; 05-13-2015, 03:05 AM. -
Installation of bowtie2 with multithreading failed
Hi
I am in need of running the bowtie2 with enabled multithread option on a linux cluster. I do not have the root access.
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