Understanding Samtools Flagstat Output
The following is the output of samtools flagstat command on bam file (paired-end) generated after markDuplicate of Picards.7417232 + 0 in total (QC-passed reads + QC-failed reads) 287618 + 0 duplicates...
View ArticleIs 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 ArticleAlign Paired End Reads Using Blast
Hi all, Has anyone align illumina paired end reads using BLAST, I used gsnap to do the alignment first, then use BLAST to align the reads which were not mapped by gsnap. It seems that BLAST can only...
View ArticleJoining Paired-End Illumina Raw Reads
I recently have amplicons sequenced (Illumina PE250) to investigate microbial community. I want to know what quality detection, and what kind of trims of raw reads by what programs should be performed...
View ArticleDoes Every Read In Paired-End Sam File Have The 0X0001 Flag?
Hello everyone, I have a simple, generic, question about SAM format flags in paired-end Illumina data. Does every read in a SAM file from a paired-end sequencing run automatically have the 0x0001 flag?...
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 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 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 simulate paired-end reads and report where each read come from
Hi all, Could you give me some suggestions for tools that simulate paired-end read data, for each read, the tool will also output the coordinate of genome, where the read comes from. Right now...
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 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 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 ArticleMerging 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 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 ArticleTophat - Understated Number Of Reads In The "Align_Summary.Txt" File
Hi all. I'm working with paired-end rna-seq data to assemble transcriptome of my species of interest. I've just realized that Tophat is understating the number of reads that I actually have and...
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 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 ArticleBest way to map paired-end, uniquely mapped reads with Bowtie2?
This has come up before, but I have never been satisfied with, or completly understood, the answers. My issue is how can Bowtie2 be used to map uniquely mapping paired-end reads (Illumina) to a genome...
View ArticlePair End Sequencing Problem
Dear all,I have a quick question on pair end sequencing. I used to work with Illumina without the pair end reads and I have dificulties to understand how the pair end reads work.In the "old" system you...
View ArticlePaired-End Reads Alignment For Variant Calling ?
I'm trying to do variant calling (SNPs, Indels) from exome-sequencing data, and the sequencing was done with paired end reads. I would like to use BWA for mapping/alignment, followed by PiCard and GATK...
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