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How To Determine If Library Is Strand-Specific

Hello all, this might be a very basic question but I gave it some thought and don't see a satisfactory answer.Let's say I have a FASTQ file from a sequencing experiment. How can one quickly determine...

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Does The Mapping Of A Read'S Pair Affect Its Own Mapping Score In Bwa?

I would like to know more about how BWA treats the mapping score of paired end reads. I am familiar with the process used to assign mapping scores by BWA (thanks to this post). I see that the mapping...

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Gsnap: How To Output Only Alignments With Minimal Number Of Mismatches?

I am aligning paired-end ChIP-Seq data of drosophila transcription factors.I would like to have a .sam file with the following alignments reported: - A maximum of three mismatches, i.e. three wrong...

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Aligning Reads To Specific Chromosome Using Bwa

Hello Everyone,I have whole genome illumina paired end reads and I want to align my reads to specific chromosome (chr 21) using BWA. I was thinking of aligning the entire reads to fasta file of the...

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Identifying mutations from Paired-End Sequencing data

Hello! I'm trying to get mutations from paired-end sequenced reads aligned with BWA  using SamTools. Coverage is about 16,000. Generally it works fine, but in one fragment (TGGGC) i see that in reads...

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How To Interpret Crossbow Data

Hello,May I know how to interpret Crossbow output. Is there any chance of building a SAM or BAM file from Crossbow output. I am looking into genome mapping. I know there are many tools available for...

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Sequence Variation Detection For Prokaryotic Genomes

I have resequenced a bacterial genome using SOLiD paired end reads. After looking at SNPs and small Indels, I'm now interested in large Insertions/Deletions (Size of genes and gene clusters).Which...

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Best Cnv Software?

Hello,I know there are many reviews out there, but I can't seem to find exactly what I like.I found this software called mrCaNaVaR, and it's great since it has it's own aligner which is supposed to be...

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Paired End Vs Single End Detection

Hi, I am wondering if anyone has a subroutine or function (hopefully in Perl or pseudocode) to detect whether a fastq file is a shuffled paired-end or not. I think I've seen a few different syntaxes on...

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Paire-End Alignments And Scripture

Hello, I am slowly getting my hands on Scripture and have stumbled on yet another unclear (at least to me )detail. I have paired-end data and the two pairs are in a sigle TopHat-derived *.bam file. I...

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Dealing With Read Counts Under Pe And Se Scenarios

Hi, I am unsure how to deal with this case to go about analysing RNA-seq data. Suppose that you have a control and treatment setup with 4 biological replicates each. However, two in control and two in...

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Is There An Elegant Way To Extract Only The Properly-Paired Reads In A...

I know I should be filtering for the following tags: 99,163,83,147 and I know that samtools would work to get all the pairs. For example:samtools view -F 0x99 -b in.bam I was wondering if there was a...

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Filter Paired-End Sam File For Xt:A:U

Dear all,I have a sam file (BWA output, paired-end reads). I would like to retain only reads which are "properly paired". This I would do by:samtools view -f 0x002 file.sam >...

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Is There Any Advantage Of Paired End Sequencing For Chip-Seq?

Hi,I hope that some of you may have a recommendation regarding the use of paired-end sequencing over single-end for ChIP-seq. In principle we expect only a minor improvement of using paired-end...

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Trinity Question

Hi, I 'd like to use Trinity to analyze my strand-specific pair-end sequencing data (dUTP) and I am very confused about how to choose the argument. I got two reads files, _1.fa and _2.fa. For...

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X And Y Chromsome Crossover Position Alignments

How do I find the genotypes on the X chromosome which match the Y SNPs listed in raw data from 23andMe, Ancestry or FTDNA

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Sorting Fastq Files After Trimming (Orphans And Pe)

I have a bunch of Illumina PE data that has been run through fastx trimmer and clipper. I am ready to map these reads, but am needing to create 2 files for paired end reads (the left and right hand...

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Estimating Insert Size From Paired End Data.

Hi,I have paired end data from illumina. To estimate the insert size in silico ( from scratch ), I have aligned the reads as single end reads to the genome ( mouse ). Now I have the two alignment files...

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Help Needed To Run Seal For Genome Mapping.

Hello, I managed to build an index file from the reference genome using Seal. Now I am trying to run Seqal but I am running into errors../seqal /user/hadoop/seal/synthetic_prq1 /user/hadoop/seal_output...

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Bwa Sampe Segmentation Fault

Hi everyone, I'm running bwa in the sampe mode and, after successfully processing >10M reads it fails with a segmentation fault (as follows) on what appears like a set of poorly-alignable reads. Any...

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