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• Errors in sam file after bwa SAMPE alignment.
  I aligned my fasta files to the reference genome using bwa sampe. I have paired end reads so fir...
• Using Bwa Sampe Using Illumna Pair End Reads
  I am trying to map illumina paired reads using BWA and I am having some trouble understanding the...
• problem with BWA alignment
  Hi, I am trying to align PE reads using bwa and something isn't working... I tried `bwa mem ref....
• Cigar And Sequence Length Are Inconsistent In Sam File
  I use bwa to algin Illumina PE reads to references, commands are: bwa aln -o 1 -l 32 -k 2 -t 16 ...
• Error with samtools index command
  Hello everyone, I am fairly new to bioinformatics. I am currently learning the command line and ...
• 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: ...
• bwa sampe: paired ends with different names
  I'm trying to align sequences I downloaded from the SRA with the dmel reference genome. After I a...
• How to find the insertion sequence in .bam file?
  I come up to aligning the fastq file based on the reference and as a result, I got the aligned ba...
• Bwa producing no alignment
  I am dealing with Illumina paired-end, 150 bp read-length datasets. Here's what my fastq files ...
• Piping With Samtools, Bwa And Bedtools
  In this tutorial I will introduce some concepts related to unix piping. Piping is a very useful f...
• Piping Bwa And Samtools
  Hi, Can someone tell me how to pipe bwa and samtools to get to a pileup2fq from a "bwa sampe"? I...
• producing a combined .sam file using *_1.sai and *_2.sai
  Hi everyone! I am aligning whole genome sequence paired reads for which I used the following com...
• Difference Between Mapped And Unmapped Reads
  Hello, I aligned paired-end files with BWA. BWA's sam file contain all reads, whether they hit t...
• bwa mem vs bwa aln
  Hello, My data is 100bpx2 HiSeq PE reads, some PE overlap so I merged them into SE. For my anal...
• Running BWA on single-end data (i.e. only one fastq file) with "sampe" option
  Hi all - I'm basically trying to replicate an alignment procedure from a paper. My data is in an ...
• Write Script To Combine All Steps Of Bwa
  For BWA, first do alignment (generate .sai), then sampe the paired-ends (generate .sam), then con...
• SGA Assembler Indexing Error
  Trying to index fastq reads but getting error Already preprocess fastq file using sga preprocess ...
• bwa samse: invalid option 'R'
  When creating .bam files from single-end read fastq's, I ran into difficulties with mutect becaus...
• Sequence Number Count In Fastq.Gz File
  Do we have any easy, fast way to know how many sequences contained in paired-end fastq.gz file? O...
• HLAminer problem with output file
  I have two different sets of WGS breast cancer data from two different experiments and am trying ...
• PE alignment with bwa aln and conversions
  So I've got paired-end read files: s1_R1.fq and s1_R2.fq 1. I align to some indexed reference w...
• Seeing Unexpected Characters (^D,^Q) In The Qual Field Of A Sam File
  i use bwa tool to map raw pair end reads to the reference, then output two sai file. then, i use...
• removing sequencing gaps
  Could anyone tell me how to remove sequencing gaps from a *.sam file?  I use bwa to map the refe...