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Question: Bowtie mapping result
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gravatar for lnaren
6 months ago by
lnaren • 10
Canada
lnaren • 10 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 • 335 views
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modified 6 months ago • written 6 months ago by lnaren • 10
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gravatar for Jennifer Hillman Jackson
6 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link modified 6 months ago • written 6 months ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for lnaren
6 months ago by
lnaren • 10
Canada
lnaren • 10 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 COMMENT • link written 6 months ago by lnaren • 10
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