Quantcast
Channel: Post Feed
Browsing all 3231 articles
Browse latest View live

Download 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 Article


Tophat 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 Article


In 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 Article

Aligning 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 Article

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 Article


X And Y Chromsome Crossover Position Alignments

How do I find the genotypes on the X chromosome which match the Y SNPs listed in raw data from 23andMe, Ancestry or FTDNA

View Article

Should 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 Article

BWA 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 Article


Merging 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 Article


Basic Paired-End Sam Questions

I can't seem to find answers to 2 very basic questions.For a paired-end sam, is there a separate sam line for mate1's and mate2's? If so, how do find the mate of a given sam line?Thanks

View Article

How 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 Article

How does the calculated inner-distance between reads change after trimming...

If we had an insert length of 426bp and an adapter size of 65bp, then the length of the central region between two 100bp reads would be 96bp (426bp - 130bp - 100bp - 100bp). So providing the mean...

View Article

Hg19 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 Article


How To Extract Information From Fastq Pair End Files

dear BioStars users,I would like to extract from my pair-end fastq files information how many times my read is occurring in my fastq file. So output could look - my read (sequence) - how many times I...

View Article

Bfast 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 Article


Counting sense reads in bacterial paired-end RNA-seq data

Hi, I'm trying to count reads mapping to sense strand. I have doubts which counts file I should chose from this pipeline. I think is "plate_R.counts" because has more reads counted in total. Am I...

View Article

How 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 Article


Assembly Aligned Paired-End Reads

Hi all,I have a set of mapped paired-end reads and I would like to assemble the ones that overlap respecting the pairing information.This means assemblying only pairs when the 2 first mates overlap and...

View Article

Macs 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 Article

Is There Any Advantage Of Paired End Sequencing For Chip-Seq?

Hi,I hope that some of you may have a recommendation regarding the use of paired-end sequencing over single-end for ChIP-seq. In principle we expect only a minor improvement of using paired-end...

View Article
Browsing all 3231 articles
Browse latest View live