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• bwa sampe error [fread] Unexpected end of file
  I am running following command to convert paired end .sai output of bwa aln to one sam file: ...
• How to blast a paired end fastq file?
  Hello everyone, I have a paired end fastq file and I know that BLAST+ in command line, accepts fa...
• How Can I Use Mate-Pair Sequences For Soapdenovo?
  Hi all, I want to assemble paired-end sequences and mate-pair sequences (HiSeq2000) together usi...
• sra to fastq
  How does SRA file looks and how is it converted into two fastq file in case of paired end?
• Aligning two genomes in fastq.gz
  Hi I would like to find the variants among two different genomes (both are paired end reads). I...
• need to separate read1 and read2 to run tophat2
  I have paired-end RNA-Seq data - read1 and read2 - stored in the same fastq file. I'd like to al...
• BAM to individual chromosome fasta/fastq
  Hi all, I have a BAM (paired end) file which i want to convert to individual chromosome fasta or...
• How should I use skewer to trim paired end reads?
  I'm attempting to use skewer to trim paired end ChIPseq fastq files. I'm not solid on how to actu...
• how to count the nucleotide frequency of paired ended fasta files
  I have read this https://www.biostars.org/p/289847/ which is very interesting. however, the fastq...
• Format Conversion: Pgf (Probe Group File) Format To Fastq
  Is anybody know how to convert pgf (probe group file) format to fastq or fasta format?? Thanks a...
• Illumina Raw sequencing data conversion to single fastq file
  I was given data in two formats, one in 18 fastq files separated as each pair end, and then raw d...
• prepare pair-ended reads for peak calling
  Hi, I have a some ChIP-seq data sets (FASTQ files) that I want to prepare for peak calling. I did...
• Why Pair Ends Data'S Ecah Pair'S Alignment Statistic And The Sum Of Them Are Different
  I have a sample's data, using illumina 's Piar End sequencing technology. RE19E2T40PA_L1_I040.pa...
• From bam paired files to fasta
  Hii people, I have paired-end sequence read of my target species which I have mapped to the refe...
• Given A Fastq File, Is It Possible To Know If It Comes From Paired Or Single End?
  Is there a FASTQ read naming convention for naming paired/single end reads? If it is the case, is...
• Fasta/Fastq File Conversion To Sff File
  Hi Can anyone help to find the script or tool to convert fasta/fastq file to sff format? Thanks ...
• repaq: compress Illumina FASTQ to be as small as 1/4 of the gzip format.
  `repaq` is an open source tool for FASTQ compression: https://github.com/OpenGene/repaq It repac...
• my bam file contains both single-end and paired-end. How can I convert bam to fastq so that fastq contains only paired-end reads?
  Hi I have a bam file that contains both single and paired-reads. How can I convert bam to fastq...
• Shrimp Short Reads Aligner
  Hey all, I've recently been introduced to short reads mapping and is planning to try on SHRiMP v...