Dealing 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 There An Elegant Way To Extract Only The Properly-Paired Reads In A...
I know I should be filtering for the following tags: 99,163,83,147 and I know that samtools would work to get all the pairs. For example:samtools view -F 0x99 -b in.bam I was wondering if there was a...
View ArticleHow To Read Maq Paired-End Alignemnt Data Using Bioconductor Packages
Hi all I have maq paired-end alignment files that I want to read into R. I have tried to browse several packages and they all seem to depend on ShortRead package of bioconductor which does not...
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 ArticlePaired-End Protocol For Micrornaseq
In another post, a guy wanted to know how to analyze paired-end data and use them to predict microRNAs.I never heard about a paired-end protocol for miRNAseq and would be interested in some more...
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 ArticleIn Paired-End Data, If One Read Of The Pair Is Unmapped, Is That Pair...
Hello everyone, I have a simple question about generic paired-end Illumina data. If one read of a pair is unmapped, does this automatically mean that the pair is improper and is (un)flagged in a SAM...
View Article20 Mate Alignment With Gaps To Reference Genome
I'm trying to align a string of twenty 5-mers with gaps of 100 to 400 bp to a reference genome. It's similar to paired-alignment except instead of N=2, N=20. The order of the twenty 5-mers is known. Is...
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 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 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 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 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 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 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 ArticleBwa Sampe Segmentation Fault
Hi everyone, I'm running bwa in the sampe mode and, after successfully processing >10M reads it fails with a segmentation fault (as follows) on what appears like a set of poorly-alignable reads. Any...
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 ArticleCombination Of Paired-End And Single-End Samples In Chip-Seq Tf Study
I have 2 batches of chip-seq samples:(A) One biological SE replicateThis batch, actually, consists of 4 SE Chip-seq samples - one treatment, one control, both have IP controls. All are SE sequenced at...
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 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...
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