Question: Bowtie mapping result
0
gravatar for lnaren
6 months ago by
lnaren10
Canada
lnaren10 wrote:

Hello, I used "Map with Bowtie for Illumina" tool to map the sequences reads to the reference genome and didn't change any settings (commonly used). Just wondering does the mapping results contain unmapped reads? After the work done, it showed "Map with Bowtie for Illumina on data 59 and data 5: mapped reads". Because it has "mapped reads" in there, I was guessing the unmapped reads already been removed. Am I correct?

Thank you very much, Ren

filter bowtie sam bam chip-seq • 334 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by lnaren10
1
gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Unmapped reads (if any) are included. Those can be filtered out with any of these tools:

  • NGS: Picard > FilterSamReads include or exclude aligned and unaligned reads and read lists
  • NGS: BamTools > Filter BAM datasets on a variety of attributes
  • NGS: SAMtools > Filter SAM or BAM, output SAM or BAM files on FLAG MAPQ RG LN or by region

The BAM/SAM from this tool will need to be coordinate sorted before using the above tools.

ChIP-seq analysis is covered in these Galaxy tutorials (using BWA instead):

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 6 months ago • written 6 months ago by Jennifer Hillman Jackson25k
0
gravatar for lnaren
6 months ago by
lnaren10
Canada
lnaren10 wrote:

Thank you very much Jen! Just wondering is there any tutorial for checking the enrichment of methylation on histone by using ChIP-seq?

ADD COMMENTlink written 6 months ago by lnaren10
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