Does The Mapping Of A Read'S Pair Affect Its Own Mapping Score In Bwa?
I would like to know more about how BWA treats the mapping score of paired end reads. I am familiar with the process used to assign mapping scores by BWA (thanks to this post). I see that the mapping...
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 ArticleResampling Fastq Sequences Without Replacement
Hello, I want to extract a random sample (without replacement) of 7.5 million fastq sequences from illumina sequencing data that contains about 30 million sequences each in of the reads. I want to...
View ArticleHow To Interpret Crossbow Data
Hello,May I know how to interpret Crossbow output. Is there any chance of building a SAM or BAM file from Crossbow output. I am looking into genome mapping. I know there are many tools available for...
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...
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 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 Articlejoin non-overlapping paired-end reads
I have a batch of illumina paired end reads with a shorter than anticipated reverse sequence for a ~550bp amplicon.The joining tools which I have used before (i.e. USEARCH, ea-utils) talk about merging...
View ArticleSamtools Count Paired-End Reads
Hi, I used tophat to align paired-end reads from an rna-seq experiment and I obtained an accepted_hits.bam alignment file. Using the accepted_hits.bam I'd like to count the number of properly aligned...
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 ArticleBasic 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 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 ArticleShould 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 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 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 ArticleWhy Pair Ends Data'S Ecah Pair'S Alignment Statistic And The Sum Of Them Are...
I have a sample's data, using illumina 's Piar End sequencing technology.RE19E2T40PA_L1_I040.pairPrimer_1.fastq (Read1) RE19E2T40PA_L1_I040.pairPrimer_2.fastq (Read2) I have aligned both Read1 and...
View ArticleHow To Rearrange Paired End Bam File?
Hello all,I have a paired end bam file and I want to use bedtools for them. After merging, the paired end read alignments are not lying next to each other. It is making problems in the bedtools...
View ArticleGsnap: How To Output Only Alignments With Minimal Number Of Mismatches?
I am aligning paired-end ChIP-Seq data of drosophila transcription factors.I would like to have a .sam file with the following alignments reported: - A maximum of three mismatches, i.e. three wrong...
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 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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