BOL

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  

Thanks but it does not accept both fastq files

NGS data are just a bunch of sequences, you have no idea which region in the genome each sequences comes from, which gene it represents...To know that you have to align the sequences to the reference sequence. The reference sequence is in most cases...

Did you followed fastuniq help $ fastuniq-i : The input file list of paired FSATQ sequence files [FILE IN]Maximum 1000 pairs This parameter is used to specify a list of paired sequence files inFASTQ format as input, in which two adjacent files...