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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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Does Order Within Read Pairs In Interleaved Files Matter?

I have now ended up with interleaved paired-end read files where the order of reads is not the same throughout the file, ie. sometimes the forward read is first, sometimes the reverse read is first,...

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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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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 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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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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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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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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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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Assembly Aligned Paired-End Reads

Hi all,I have a set of mapped paired-end reads and I would like to assemble the ones that overlap respecting the pairing information.This means assemblying only pairs when the 2 first mates overlap and...

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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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Pair End Sequencing Problem

Dear all,I have a quick question on pair end sequencing. I used to work with Illumina without the pair end reads and I have dificulties to understand how the pair end reads work.In the "old" system you...

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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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What Better Way To Get The Paired Reads Aligned Against The Reference Genome?

Hi everybody,I have a group of paired reads sequenced using Solid 4 (50bp each mate). I discovered that reads are contaminated by E.coli. My strategy is to align the reads against the reference genome...

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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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20 Mate Alignment With Gaps To Reference Genome

I'm trying to align a string of twenty 5-mers with gaps of 100 to 400 bp to a reference genome. It's similar to paired-alignment except instead of N=2, N=20. The order of the twenty 5-mers is known. Is...

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Align Paired End Reads Using Blast

Hi all, Has anyone align illumina paired end reads using BLAST, I used gsnap to do the alignment first, then use BLAST to align the reads which were not mapped by gsnap. It seems that BLAST can only...

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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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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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