Tool 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 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 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 ArticleHow 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 ArticleHow 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 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 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 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 ArticleSequence Variation Detection For Prokaryotic Genomes
I have resequenced a bacterial genome using SOLiD paired end reads. After looking at SNPs and small Indels, I'm now interested in large Insertions/Deletions (Size of genes and gene clusters).Which...
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 ArticleDna Sequencing Using Abyss-Pe Of Paired End Reads
Hello! I've got to run abyss-pe on 2 files I've got and find the best parameters (k and so on) that would create the best contig coverage (sorry if I'm messing things up, I'm a programmer that had a...
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 ArticlePaired-End Bam Files
Hi,Having two BAM files from NGS data, how can one check if they are the BAM files (left and right) from a paired end mapping of the same sample? Thanks for the help.
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 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 ArticleForum: Attempting to understand pair end sequencing, mainly illumina
Hi I am currently attempted to understand how pair end sequencing works. I understand the basics that it sequences from both ends and if there is an overlapping region they can be joined to create...
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 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 ArticleIdentifying mutations from Paired-End Sequencing data
Hello! I'm trying to get mutations from paired-end sequenced reads aligned with BWA using SamTools. Coverage is about 16,000. Generally it works fine, but in one fragment (TGGGC) i see that in reads...
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...
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