BOL

Thanks for developing geneSCF, I tried to install it but got the following error bio@bio214b[geneSCF-master-source-v1.1-p2] ./prepare_database [] prepare_database USAGE: ./prepare_database...

A tetra-nucleotide is a fragment of DNA sequence with 4 bases (e.g. AGTC or TTGG). Pride et al. (2003) showed that the frequency of tetra-nucleotides in bacterial genomes contain useful, albeit weak, phylogenetic signals. Even though...

Thanks everyone, it is done :) bio@bio214b[bio] fastq-stats out.R1.fq []reads 39376969len 251len mean 251.0000len stdev 0.0000len min 251phred 33window-size 2000000cycle-max 35dups 1609486%dup 4.0874unique-dup seq 23609min dup count 2dup seq 1...

I recomment reformat.sh dedupe.sh from BBmap suits (https://sourceforge.net/projects/bbmap/)

You can follow following steps to get rid of duplicates: a. Extract all the reads Ids for indivisual pair and make it uniq.  b. Use uniq Ids to extract the original reads from fastq files (Seq.R1.fastq/Seq.R2.fastq in your case).  

You can follow following steps to get rid of duplicates: a. Extract all the reads Ids for indivisual pair and make it uniq.  b. Use uniq Ids to extract the original reads from fastq files (Seq.R1.fastq/Seq.R2.fastq in your case).  

You can follow following steps to get rid of duplicates: a. Extract all the reads Ids for indivisual pair and make it uniq.  b. Use uniq Ids to extract the original reads from fastq files (Seq.R1.fastq/Seq.R2.fastq in your case).  

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...

FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. Both the sequence letter and quality score are each encoded with a...

Show before(B) and after(A) the matching region $ grep -B 3 -A 2 foo README.txt #Linux #Tricks #View #Grep

Perl OneLiner http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/oneliners.html #Perl #Oneliner #NGS #Script

NGS onliner http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/subsetFASTAFASTAQ.html #OneLiner #NGS

Ok !  fastuniq accept the name of fastq as a listfile. Create a listfile.txt and write both of your PE file name there, and call it with -i listfile.txt