Results for "duplicates"
Blogs
BBTools for bioinformatician !
...in=assembly1.fa,assembly2.fa out=merged.fa That will absorb exact duplicates and containments. You can use...a read came from; in other words, it can't remove only reads that are duplicates across multiple files but lea...2268 days ago
Bookmarks
- ...ed. Then select one or more output types and add your identifiers in the ID list box. Set the remove duplicate values to 'No' if you do not want duplicates to be removed. Clicking on su...
2892 days ago
jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
...a reads, as well as reads from Pacific Biosciences These simulations include sequencing errors, mapping qualities, multiplexing, and optical/PCR duplicates. All outputs can be written t...1743 days ago
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News
Genome of Rainbow Trout Sequenced
...here are fewer duplicated genes still present. Most of the duplicated genes get lost or modified so much that they are no longer recognizable as duplicates over time. In the trout and s...3661 days ago
Bio-Scripts
Samtools commands for bioinformatician !
...total+=1}END{print (total/c)*100}' ### flagstat # output file has two columns: QC-passed reads and QC-failed reads # and rows: total reads, duplicates, mapped. samtools flagstat s...1601 days ago
Bash script to alignment of short reads against reference genome !
...w.bam --- sort the BAM file, writing it to .sorted.bam. #marking PCR duplicates: sambamba markdup SRR1770413....SRR1770413.bam --- this marks reads which appear to be redundant PCR duplicates based on their read mapping p...1557 days ago
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Tags
- I wanted to remove the duplicates from fastq file. I planned to use fastuniq but it does not have good tutorial. Can you please tell me how to use it? http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0052249
Tags: fastq, fastuniq, duplicates, NGS
2558 days ago
How to remove duplicates reads Ids ?
I mapped reads with bwa mem -M -t 40 allCombinedFinalSet.fa Seq.R1.fastq Seq.R2.fastq > aln.sam Extracted the mapped reads samtools view -f 0x2 -b aln.bam > output.bam Extracted the fastq bamToFastq -i output.bam -fq R1.fq -fq2 R2.fq grep @HISEQ578:1035:HJ2KCBCXX:1:1104...Tags: Reads, Ids, NGS, Fastq, Duplicates
2557 days ago
Comments
Comment on "R and Bioconductor Tutorial"
NGS with R ShortRead – Quality assesment of the reads, finding duplicates, trimming, string pattern searches [1] Biostrings – Reading sequences in R [2] BSGenomes &ndas...3668 days ago
