I'm having a problem with aligning Illumina PE reads with BBMap version 35.92.
Execution of
Code:
bbmap.sh
77 results in 0.0088 seconds.
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BBMAP paired-end alignment problem
Hi All
I'm having a problem with aligning Illumina PE reads with BBMap version 35.92.
Execution of
... -
BBMAP paired-end alignment problem
Hi All
Trying to use bbmap to align some Illumina PE reads. My command line looks like this
...Code:bbmap.sh overwrite=t ref=A.fasta
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how do i reduce misassemblies in spades?
I'm new to spades and i've started on some genomes which i previously assembled in velvet (~6 Mb chromosome plus one ~40 Kb plasmid, and a few long repeats... -
strand specificity of stranded illumina paired-end libraries
Hello
I recently analysed stranded illumina trueseq paired-end RNA-seq data. My data is 1+-,1-+,2++,2--, meaning the second_in_pair should... -
IDBA 'std::logic_error'
Hi, I am trying to merge paired-end illumina reads (read length: 101) .
I am using the command:
fq2fa --merge --filter sample_1.fq... -
Trimmomatic adapter file vs Custom made file
Hello everyone,
I am working with TruSeq paired end data (150bp). I have a doubt regarding the adapter file provided in Trimmomatic... -
FastQ: trimming paired reads down to a set length
Hello,
I have some 2x300bp sequencing data and I want to treat it as if it were a 2x100bp run.
So, I have some paired-read... -
MISO: Best-guessing insert size and stddev versus running single-ended for PE data
I am conducting a miso analysis for a single gene on a large number of Paired End RNAseq bams that is spread out on several external HDs (twenty 4tb drives).... -
Brainstorming: Error sources for Cuffquant failure: Map Mass: 0.00
Hello folks,
I have an issue with Cuffquant v2.2.1, which fails to quantify the expression (create .cxb files) of the current RNA-seq I am...Last edited by Thias; 07-22-2016, 02:33 AM. -
Consider dovetail pairs as concordant pairs?
Hi, all
Recently I have a paired-end data from Illumina/Solexa sequencing machine. My sequencing DNA fragments are about 100-300 bp, and... -
Problem somewhere during paired-end seq analysis -> no reads mapped
Hello everybody,
this is my fist time to try to handle to analyze paired-end sequencing files.
Finally BamCoverage complained there... -
Mixing paired-end and single-end reads in Tophat: Do I have to reverse the SE-reads f
This is a cross-post from the Tuxedo Google group: https://groups.google.com/forum/#!to...rs/BtI3_fp_n-o
And a follow-up... -
Prinseq-lite problem
Dear all,
I am using prinseq (v.0.20.4, CentOS) to filter my paried end data with the following commands.
[root@localhost]# perl prinseq-lite.pl...Last edited by kumar03; 12-09-2015, 06:40 PM. -
Paired-end Illumina reads preprocessing with Trimmomatic
Dear all,
I have few questions about the trimming of adapters with Trimmomatic. I have 2x150 bp paired end runs from Illumina MiSeq system.... -
Samtools MPILEUP on single-end/paired-end data
Hi everybody,
for variant calling, i am using samtools mpileup.
as far as i know, mpileup is by default ignoring certain...
