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...
View ArticleRoche 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...
View ArticleBest way to map paired-end, uniquely mapped reads with Bowtie2?
This has come up before, but I have never been satisfied with, or completly understood, the answers. My issue is how can Bowtie2 be used to map uniquely mapping paired-end reads (Illumina) to a genome...
View ArticleIdentifying mutations from Paired-End Sequencing data
Hello! I'm trying to get mutations from paired-end sequenced reads aligned with BWA using SamTools. Coverage is about 16,000. Generally it works fine, but in one fragment (TGGGC) i see that in reads...
View ArticleJoining 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...
View ArticleHelp 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...
View ArticleWarnings 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...
View ArticleBasic 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
View ArticleCrossbow 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...
View ArticleChIPseq paired-end bowtie2 concern regarding biological replicates
I am working with ChIP-seq paired-end data where there is concern that one or more of the biological replicates may not be very good, but it is unknown which replicate may have a problem (I suspect...
View ArticleTool: 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...
View ArticleTake A Subset Of A Fastq Paired-End Sample
Hi,I have two paired-end fastq compressed files coming from HiSeq RNA-SEq experiment, ie., pair.1.fastq.gz and pair.2.fastq.gz.The files are very large so I wanted to just take a few million/thousand...
View Articletool simulate paired-end reads and report where each read come from
Hi all, Could you give me some suggestions for tools that simulate paired-end read data, for each read, the tool will also output the coordinate of genome, where the read comes from. Right now...
View ArticleClik here to view.
Trinity Question
Hi， I 'd like to use Trinity to analyze my strand-specific pair-end sequencing data (dUTP) and I am very confused about how to choose the argument. I got two reads files, _1.fa and _2.fa. For...
View ArticleAssembly 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...
View ArticleUnderstanding 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...
View ArticleWhy Pair Ends Data'S Ecah Pair'S Alignment Statistic And The Sum Of Them Are...
I have a sample's data, using illumina 's Piar End sequencing technology.RE19E2T40PA_L1_I040.pairPrimer_1.fastq (Read1) RE19E2T40PA_L1_I040.pairPrimer_2.fastq (Read2) I have aligned both Read1 and...
View ArticlePaired-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...
View ArticleMacs 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...
View ArticleX And Y Chromsome Crossover Position Alignments
How do I find the genotypes on the X chromosome which match the Y SNPs listed in raw data from 23andMe, Ancestry or FTDNA
View Article