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Trinity Question
Hi， I 'd like to use Trinity to analyze my strand-specific pair-end sequencing data (dUTP) and I am very confused about how to choose the argument. I got two reads files, _1.fa and _2.fa. For...
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 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 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 ArticleAnalyzing Older Illumina Paired-End Data
Hi all, I've got some reads from mid-2010 that I'd like to re-align. I'm not sure how best to proceed. These are from a Illumina Genome Analyzer IIx. They're 40-bp, paired-end. Here's what the text...
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 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 ArticleHigh level of duplicate in one reads of paired-end data
Hi,We are doing some transcriptomic analysis on bovine immune blood cells and we seem's to have some problem with high levels of duplicate in our data. Our library were prepared with the illumina...
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 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 ArticleCounting Reads On Paired-End Strand-Specific Rnaseq Data
Hello everybody, I've a strand-specific paired-end library on which I'd like to perform some standard DGE analysis. However I'm quite unclear about how to go about counting reads. Usually when I have a...
View ArticleWgsim Mutations In Output After Setting Everything To 0
I was just wondering, is there any useful information on wgsim? Tutorial? Anything? I have been stuck with it for the last 2 weeks. I'm really not sure how to use it. I need it for a project of mine....
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 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 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 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 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 ArticleEstimating Insert Size From Paired End Data.
Hi,I have paired end data from illumina. To estimate the insert size in silico ( from scratch ), I have aligned the reads as single end reads to the genome ( mouse ). Now I have the two alignment files...
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...
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