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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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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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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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Resampling Fastq Sequences Without Replacement

Hello, I want to extract a random sample (without replacement) of 7.5 million fastq sequences from illumina sequencing data that contains about 30 million sequences each in of the reads. I want to...

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Combination Of Paired-End And Single-End Samples In Chip-Seq Tf Study

I have 2 batches of chip-seq samples:(A) One biological SE replicateThis batch, actually, consists of 4 SE Chip-seq samples - one treatment, one control, both have IP controls. All are SE sequenced at...

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Trimming Adapters For Paired-End Sequences

Hi all,I got illumina paired end fastq files. They told me to trim read 2 at the beginning for ~20 to 30 bp due to the WGA adapters. Can we find the adapters by looking in to the quality? Which tool is...

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Estimating Insert Size From Paired End Data.

Hi,I have paired end data from illumina. To estimate the insert size in silico ( from scratch ), I have aligned the reads as single end reads to the genome ( mouse ). Now I have the two alignment files...

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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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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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Joining Paired-End Illumina Raw Reads

I recently have amplicons sequenced (Illumina PE250) to investigate microbial community. I want to know what quality detection, and what kind of trims of raw reads by what programs should be performed...

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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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Paired-End Protocol For Micrornaseq

In another post, a guy wanted to know how to analyze paired-end data and use them to predict microRNAs.I never heard about a paired-end protocol for miRNAseq and would be interested in some more...

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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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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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High level of duplicate in one reads of paired-end data

Hi,We are doing some transcriptomic analysis on bovine immune blood cells and we seem's to have some problem with high levels of duplicate in our data. Our library were prepared with the illumina...

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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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Amos With Paired End Data

Hi all, how do I take advantage of paired end data with AMOS? I have a 2x100bp fastq file that I would like to use AMOScmp-shortreads with. I see that when I google for it, there might be a .mates file...

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Is There Any Advantage Of Paired End Sequencing For Chip-Seq?

Hi,I hope that some of you may have a recommendation regarding the use of paired-end sequencing over single-end for ChIP-seq. In principle we expect only a minor improvement of using paired-end...

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Counting reads for gene in bacterial genomes

Hi,I'm analyzing paired-end expression libraries of E. coli and wanted to get some advise about how to count the number of reads for each gene. After mapping the reads to the genome I use htseq-count...

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Samtools Mpileup And Overlapping Paired-End Reads

I am using samtools mpileup to generate a pileup for paired-end RNA sequencing data. I am curious about how samtools handles pair mates whose read mappings overlap. With regard to the simple example...

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