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In Paired-End Data, If One Read Of The Pair Is Unmapped, Is That Pair...

Hello everyone, I have a simple question about generic paired-end Illumina data. If one read of a pair is unmapped, does this automatically mean that the pair is improper and is (un)flagged in a SAM...

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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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Aligning Paired-End Reads In Single-End Mode

Hello,I have a question on how to align paired-end reads.In cases of very large fastq files, which make aligners like TopHat crash in a server with limited memory in RAM, I have seen people align one...

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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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Wgsim Mutations In Output After Setting Everything To 0

I was just wondering, is there any useful information on wgsim? Tutorial? Anything? I have been stuck with it for the last 2 weeks. I'm really not sure how to use it. I need it for a project of mine....

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Counting Reads On Paired-End Strand-Specific Rnaseq Data

Hello everybody, I've a strand-specific paired-end library on which I'd like to perform some standard DGE analysis. However I'm quite unclear about how to go about counting reads. Usually when I have a...

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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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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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Using Paired End And Orphaned Singles For De Novo Assembly

I have been using FastX to process reads prior to de novo assembly and mapping. What I have discovered and few have pointed out is the FastX will delete reads leaving reads unpaired which changes the...

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Merging Illumina Paired End Reads

Dear All,I have fastq a dataset containing forward and reverse sequences obtained through paired end module of Illumina platform. I am trying to merge these paired end reads. I have a query which I...

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Fastq Sort By Sequence

Dear all,I have some questions about manipulating fastq files. Its the first time I do this, so I want advice, how to do it. Its a special case, because I only want to keep reads when the following...

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Basic Paired-End Sam Questions

I can't seem to find answers to 2 very basic questions.For a paired-end sam, is there a separate sam line for mate1's and mate2's? If so, how do find the mate of a given sam line?Thanks

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Coverage For Pair-End Rna-Seq, Extend Reads Or Not?

HI, all I have a question when computing region coverage of pair-end RNASeq data. As showed by the sketch map, when computing region coverage, whether I should use actually mapped reads or extended...

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How To Assemble Genome Generated With Bac Clones?

I have 2 fastq files from illimina with reads length 250b. Sequences from one file obtained by sequencing from "right" and from "left" in another. This is paired end sequencing. As it is whole genome...

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Mapping Trimmed Paired End Reads With Mapsplice

Hi! I'm trying to map illumina paired end using MapSplice. I used script named sickle to trim the bad quality tails and the output looks like this:Paired end 1@TUPAC_0006:1:1:3062:1473#0/1...

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How To Extract Information From Fastq Pair End Files

dear BioStars users,I would like to extract from my pair-end fastq files information how many times my read is occurring in my fastq file. So output could look - my read (sequence) - how many times I...

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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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Collect Read Pairs Where At Least One Read Is Mapped

I might word my initial question like another post, but I really have the opposite meaning, i think:Filtering multiple flags with SAMtoolsI am trying to remove paired-end reads from a .SAM file where...

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BWA MEM mate pair rescue

Greetings,Can someone spell out what this option means?  I have several guesses, but would rather ask than guess. -P        In the paired-end mode, perform SW to rescue missing hits only but do not try...

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Paired-End Reads Alignment For Variant Calling ?

I'm trying to do variant calling (SNPs, Indels) from exome-sequencing data, and the sequencing was done with paired end reads. I would like to use BWA for mapping/alignment, followed by PiCard and GATK...

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