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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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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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Paired-End Reads Alignment For Variant Calling ?

I'm trying to do variant calling (SNPs, Indels) from exome-sequencing data, and the sequencing was done with paired end reads. I would like to use BWA for mapping/alignment, followed by PiCard and GATK...

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Need help using Shrimp2 on paired end color-space SOLiD data.

Hi, I have SOLiD reads which are paried-end (75bp and 35bp) in .csfasta and .QV.qual format. I would like to use Shrimp2 to align them. So far I have been having trouble using it. I used the following...

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Tool Recommendation Wanted For Cleaning Fasta/Fastq Files To Remove Unpaired...

Hi Everyone, I've been digging around the web trying to find a tool that would allow me to clean-up my paired-end Illumina data before mapping. My pipeline thus far has been to:1) FASTQC - my R1 file...

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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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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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Tutorial: Live on-line tutorial using Integrated Genome Browser (December 17...

“Focus on a Feature: Intro to All New Features in IGB 8.2.” When:Wednesday, December 17 at 3:30pm ESTProgram Introduction to IGB 8.2Viewing paired-end dataUsing Plug-insRunning IGB through RQ and A...

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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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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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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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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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Macs Raises Error: No Such File Or Directory

I am trying to run macs14 with sam files from paired-end data + control. Macs14 returns "No such file":sb7904313:line2 $ macs14 -t /Volumes/Data/G6L2_G6L3/s5/clean_paired_sample.sam -c...

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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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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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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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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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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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Efficiently join paired-end read coordinates in the same line?

Dear community, I have a huge paired-end HiC dataset (BAM format) which I want to format like this way: HWI-D00283:117:C5KKJANXX:2:1101:1139:77789 chr6 153338506 153338556 37 + chr6 153338031 153338081...

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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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