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Aligning Paired-End Reads In Single-End Mode

Hello,I have a question on how to align paired-end reads.In cases of very large fastq files, which make aligners like TopHat crash in a server with limited memory in RAM, I have seen people align one...

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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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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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Help Needed To Run Seal For Genome Mapping.

Hello, I managed to build an index file from the reference genome using Seal. Now I am trying to run Seqal but I am running into errors../seqal /user/hadoop/seal/synthetic_prq1 /user/hadoop/seal_output...

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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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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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Tophat - Understated Number Of Reads In The "Align_Summary.Txt" File

Hi all. I'm working with paired-end rna-seq data to assemble transcriptome of my species of interest. I've just realized that Tophat is understating the number of reads that I actually have and...

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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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Forum: Attempting to understand pair end sequencing, mainly illumina

Hi I am currently attempted to understand how pair end sequencing works. I understand the basics that it sequences from both ends and if there is an overlapping region they can be joined to create...

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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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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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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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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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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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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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Hg19 Strand Information Of Sam Output.

Hi all,I've got Paired-End Illumina data mapped against the Human Hg19. When viewing the SAM output, how can I check if a pair mapped against the forward Hg19 genome sequence or against the reverse...

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Filter Paired-End Sam File For Xt:A:U

Dear all,I have a sam file (BWA output, paired-end reads). I would like to retain only reads which are "properly paired". This I would do by:samtools view -f 0x002 file.sam >...

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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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Bwa Sampe Segmentation Fault

Hi everyone, I'm running bwa in the sampe mode and, after successfully processing >10M reads it fails with a segmentation fault (as follows) on what appears like a set of poorly-alignable reads. Any...

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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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