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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...

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Paired-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.

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Resampling 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...

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How 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...

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Paired-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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Wgsim 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....

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Take 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...

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join 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...

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Samtools 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...

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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...

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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

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Estimating 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...

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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...

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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...

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Tool: 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...

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Why 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...

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How 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...

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Gsnap: 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...

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Using 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...

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Warnings 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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