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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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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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Mapping target-enriched reads to a transcriptome reference

  Hi all, I have carried out transcriptome sequencing on a plant species and then, from the resulting assembled contigs, have designed capture probes for 970 gene regions. I then carried out...

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Understanding Samtools Flagstat Output

The following is the output of samtools flagstat command on bam file (paired-end) generated after markDuplicate of Picards.7417232 + 0 in total (QC-passed reads + QC-failed reads) 287618 + 0 duplicates...

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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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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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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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Should I merge bacterial RNA-seq paired-end data?

Hi,I have bacterial RNA-seq data from paired-end reads (2x75). I'm interested in sense/antisense differential expression.I would like to know if makes sense to merge R1 and R2 into one read (if...

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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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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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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 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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How To Convert A Soapsnp Output File To Soap, Sam Or Bam Formats

Hello,I would like to know if there is any tool to convert SOAPsnp to SOAP? Once it is converted to SOAP, I can convert it to SAM using Soap2Sam from reseqtools. Hopefully using reseqtools is not that...

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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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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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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 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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What Does Requirebothendsmapped From Rsubread Package Means?

Hi,I am using the featureCounts from the Rsubread package. And I am trying to understand what does the requireBothEndsMapped option do. The manual says"logical indicating if both ends from the same...

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How To Read Maq Paired-End Alignemnt Data Using Bioconductor Packages

Hi all I have maq paired-end alignment files that I want to read into R. I have tried to browse several packages and they all seem to depend on ShortRead package of bioconductor which does not...

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How To Count Stand-Specific Paired-End Rna-Seq Reads Overlapping Known...

Dear BiostarsDoes any one how to overlap stand-specific paired-end RNA-Seq reads (BAM) with known protein coding genes (BED) ?I tried the following but I think it is not the correct way ? Would...

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