Samtools 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 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 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 Articlejoin non-overlapping paired-end reads
I have a batch of illumina paired end reads with a shorter than anticipated reverse sequence for a ~550bp amplicon.The joining tools which I have used before (i.e. USEARCH, ea-utils) talk about merging...
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 ArticleUsing Paired End And Orphaned Singles For De Novo Assembly
I have been using FastX to process reads prior to de novo assembly and mapping. What I have discovered and few have pointed out is the FastX will delete reads leaving reads unpaired which changes the...
View ArticleAligning 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...
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 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 ArticleFilter 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 >...
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 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 ArticleHow To Check If Illumina Fastq Is Single Or Paired End With Minimal Sequence Id
Hi all, I am trying to check if a FASTQ is single or paired end. From wikipedia I saw that default format has to be like this:@HWUSI-EAS100R:6:73:941:1973#0/1but in my case the sequence id is...
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 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 ArticlePair End Sequencing Problem
Dear all,I have a quick question on pair end sequencing. I used to work with Illumina without the pair end reads and I have dificulties to understand how the pair end reads work.In the "old" system you...
View ArticleOrientation 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...
View ArticleCollect 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...
View ArticleBfast Match Paired End Reads - Reports Half Total Number Of Reads
I'm using bfast 0.7.0a and testing on the paired end data present in the bfast user manual (Figure 5.4 in bfast-book.pdf). The format for this fastq file is shown that paired reads should follow...
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...
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