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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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How does the calculated inner-distance between reads change after trimming...

If we had an insert length of 426bp and an adapter size of 65bp, then the length of the central region between two 100bp reads would be 96bp (426bp - 130bp - 100bp - 100bp). So providing the mean...

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Crossbow Final Step Failing On Emr

Hello, I am trying to run Crossbow via EMR command line. I managed to complete all the crossbow steps- Alignment with Bowtie, Calling SNPS and Postprocess. I am getting an error in the final step Get...

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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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Download Large Paired-End Rna-Seq And Microarray Data Of The Same Sample (>...

Hi,I was trying to find if there is any large size paired-end RNA-Seq and microarray data of the same sample, but I wasn't able to find as much data as I wanted.Could somebody please point out where 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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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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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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Difference Between "Mate Pair" And "Pair-End"

Just as the title , I can't tell the difference between those two conception. :) waiting for your help.

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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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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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Tool: Trim Adapters Of Paired-End Reads (Fastq)

Trimming adapter sequences of paired-end experiments is sometimes a problem. If you clip the mates in two steps, it migh happen that you loose one mate, but not the corresponding one, resulting in two...

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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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Picard Matequery Slows Process To A Crawl

I'm looking to iterate through an indexed BAM file using picard and perform various tests on both a read and it's mate. For some I would need the full SAMRecord for the mate so I can't just use the...

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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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Bfast Match Paired End Reads - Reports Half Total Number Of Reads

I'm using bfast 0.7.0a and testing on the paired end data present in the bfast user manual (Figure 5.4 in bfast-book.pdf). The format for this fastq file is shown that paired reads should follow...

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Paired-End Bam Files

Hi,Having two BAM files from NGS data, how can one check if they are the BAM files (left and right) from a paired end mapping of the same sample? Thanks for the help.

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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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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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Mapping Applications On Hadoop Cluster

Hello,I would like to know if there are any new mapping applications for paired end data designed to work on hadoop cluster. The mapping applications that i know are CloudBurst (single ended), Crossbow...

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