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...
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 ArticleHg19 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...
View ArticlePicard 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...
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 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 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 ArticleHow To Count Stand-Specific Paired-End Rna-Seq Reads Overlapping Known...
Dear BiostarsDoes any one how to overlap stand-specific paired-end RNA-Seq reads (BAM) with known protein coding genes (BED) ?I tried the following but I think it is not the correct way ? Would...
View ArticleMerging Illumina Paired End Reads
Dear All,I have fastq a dataset containing forward and reverse sequences obtained through paired end module of Illumina platform. I am trying to merge these paired end reads. I have a query which I...
View ArticleSamtools Mpileup And Overlapping Paired-End Reads
I am using samtools mpileup to generate a pileup for paired-end RNA sequencing data. I am curious about how samtools handles pair mates whose read mappings overlap. With regard to the simple example...
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 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 ArticleMapping 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 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 ArticleWhat 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...
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 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 ArticlePaired End Vs Single End Detection
Hi, I am wondering if anyone has a subroutine or function (hopefully in Perl or pseudocode) to detect whether a fastq file is a shuffled paired-end or not. I think I've seen a few different syntaxes on...
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 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...
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