Forum: 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 ArticleExisting Tools For Post-Processing After Aligning Paired-End Reads With Blat?
Hi,I'm wondering if there are existing tools that can do post-processing on paired-end reads' BLAT output.More specifically, I'd like the tool to "merge" the alignments from the alignments of each...
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 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 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 ArticleEfficiently 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...
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 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 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 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 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...
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 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 ArticleBWA MEM mate pair rescue
Greetings,Can someone spell out what this option means? I have several guesses, but would rather ask than guess. -P In the paired-end mode, perform SW to rescue missing hits only but do not try...
View ArticleMapping Applications On Hadoop Cluster
Hello,I would like to know if there are any new mapping applications for paired end data designed to work on hadoop cluster. The mapping applications that i know are CloudBurst (single ended), Crossbow...
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 ArticleShould I merge bacterial RNA-seq paired-end data?
Hi,I have bacterial RNA-seq data from paired-end reads (2x75). I'm interested in sense/antisense differential expression.I would like to know if makes sense to merge R1 and R2 into one read (if...
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 ArticleResampling Fastq Sequences Without Replacement
Hello, I want to extract a random sample (without replacement) of 7.5 million fastq sequences from illumina sequencing data that contains about 30 million sequences each in of the reads. I want to...
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...
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