Understanding 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 ArticleHow 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...
View ArticleTool 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...
View ArticleDifference Between "Mate Pair" And "Pair-End"
Just as the title , I can't tell the difference between those two conception. :) waiting for your help.
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 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 ArticleHow 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...
View ArticleSamtools Count Paired-End Reads
Hi, I used tophat to align paired-end reads from an rna-seq experiment and I obtained an accepted_hits.bam alignment file. Using the accepted_hits.bam I'd like to count the number of properly aligned...
View ArticleCoverage For Pair-End Rna-Seq, Extend Reads Or Not?
HI, all I have a question when computing region coverage of pair-end RNASeq data. As showed by the sketch map, when computing region coverage, whether I should use actually mapped reads or extended...
View ArticleAligning Reads To Specific Chromosome Using Bwa
Hello Everyone,I have whole genome illumina paired end reads and I want to align my reads to specific chromosome (chr 21) using BWA. I was thinking of aligning the entire reads to fasta file of the...
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 ArticleTrimming 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...
View ArticleSequence Variation Detection For Prokaryotic Genomes
I have resequenced a bacterial genome using SOLiD paired end reads. After looking at SNPs and small Indels, I'm now interested in large Insertions/Deletions (Size of genes and gene clusters).Which...
View ArticleSorting Fastq Files After Trimming (Orphans And Pe)
I have a bunch of Illumina PE data that has been run through fastx trimmer and clipper. I am ready to map these reads, but am needing to create 2 files for paired end reads (the left and right hand...
View ArticleShould 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...
View ArticleForum: Mapping Of Ngs Short Reads
This is a simple explanation of how the mapping of short reads works !http://www.youtube.com/watch?v=1ZyoI-4ObSA&feature=related see the first 16 min ! It helped me a lot to understand the basic...
View ArticleTophat 2 - Both Pairs Map Concordantly
Hi,I have just run the following command tophat2 --solexa1.3-quals -p 12 -r 80 --max-multihits 1 --no-mixed --no-discordant /home/Turkey/Index/turkeyindex /home/Turkey/WTCHG24920061sequence1.fa...
View ArticleDealing With Read Counts Under Pe And Se Scenarios
Hi, I am unsure how to deal with this case to go about analysing RNA-seq data. Suppose that you have a control and treatment setup with 4 biological replicates each. However, two in control and two in...
View ArticleIs It Ok To Use One End Of A Set Of Paired-End Reads As A Set Of Single Reads?
Hi,I'm wondering if it's OK to use one end of a set of paired-end reads as a set of single reads?I just want to get a single read data set of a sample, but currently there's only paired-end data...
View ArticleDownload 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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