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How To Check If Illumina Fastq Is Single Or Paired End With Minimal Sequence Id

Hi all, I am trying to check if a FASTQ is single or paired end. From wikipedia I saw that default format has to be like this:@HWUSI-EAS100R:6:73:941:1973#0/1but in my case the sequence id is...

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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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Dna Sequencing Using Abyss-Pe Of Paired End Reads

Hello! I've got to run abyss-pe on 2 files I've got and find the best parameters (k and so on) that would create the best contig coverage (sorry if I'm messing things up, I'm a programmer that had a...

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How To Determine If Paired–End Illumina Rnaseq Reads Are Strand–Specific

I've been provided with more than a billion reads of RNAseq data for a poorly annotated nematode species. They appear to be 2x100 paired-end Illumina reads – I currently know frustratingly little about...

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Orientation in paired-end sequencing?

I am new to bioinformatics and currently learning how to use Bowtie 2. As written in the manual:  A pair that aligns with the expected relative mate orientation and with the expected range of distances...

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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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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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Tool Recommendation Wanted For Cleaning Fasta/Fastq Files To Remove Unpaired...

Hi Everyone, I've been digging around the web trying to find a tool that would allow me to clean-up my paired-end Illumina data before mapping. My pipeline thus far has been to:1) FASTQC - my R1 file...

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Does Every Read In Paired-End Sam File Have The 0X0001 Flag?

Hello everyone, I have a simple, generic, question about SAM format flags in paired-end Illumina data. Does every read in a SAM file from a paired-end sequencing run automatically have the 0x0001 flag?...

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Existing Tools For Post-Processing After Aligning Paired-End Reads With Blat?

Hi,I'm wondering if there are existing tools that can do post-processing on paired-end reads' BLAT output.More specifically, I'd like the tool to "merge" the alignments from the alignments of each...

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Counting sense reads in bacterial paired-end RNA-seq data

Hi, I'm trying to count reads mapping to sense strand. I have doubts which counts file I should chose from this pipeline. I think is "plate_R.counts" because has more reads counted in total. Am I...

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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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Tophat 2 - Both Pairs Map Concordantly

Hi,I have just run the following command tophat2 --solexa1.3-quals -p 12 -r 80 --max-multihits 1 --no-mixed --no-discordant /home/Turkey/Index/turkeyindex /home/Turkey/WTCHG24920061sequence1.fa...

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Roche 454: How to know if reads are paired ?

Hi,Imagine a Fastq file generated from a Roche 454 platform. You have no information whatsoever about the protocol that what used. The header of the reads give no specific information, just random...

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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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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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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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Warnings In Bowtie Mapping

Hello, I am trying to use bowtie on small synthetic data for short read mapping. My command is ./bowtie -p 8 -t -S hg19 -1 synthetic_sample1.fq -2 synthetic_sample2.fq > bowtie.sam. The alignment...

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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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Should We Dump Illumina Pair-End Mapping Results In Sam With Mapq=0, But Good...

hi, everyone! I am working on illumina pair-end sequencingAfter mapping by bwa, I got a pair of reads with MAPQ=0, with both reads mapped to more than one place. But the Template Length is OK, and I...

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