Question: Get multimapped reads from STAR in Galaxy.
0
gravatar for luisafermercadom
7 months ago by
luisafermercadom0 wrote:

Hi,

Using RNA STAR in Galaxy to map my yeast read back to the genome: (single end reads), I'm getting a huge number of multi-mapped reads (40-60%). I want to get those multimapped reads, so I can look at them ...

How do I write out a multi-mapped reads file from Galaxy? (We do not have an instance here.)

Thank you!

fastq rna-seq sam filter bam • 372 views
ADD COMMENTlink modified 6 days ago by sf.rocha0 • written 7 months ago by luisafermercadom0
1
gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

BAM datasets can be filtered with either of the tools below. If you want the fastq sequences, those can be extracted from the filtered BAM dataset.

Filter BAM:

  • NGS: SAMtools > Filter SAM or BAM, output SAM or BAM
  • NGS: BamTools > Filter BAM datasets on a variety of attributes

BAM/SAM to Fastq:

  • NGS: Picard > SamToFastq extract reads and qualities from SAM/BAM dataset and convert to fastq

Thanks! Jen, Galaxy team

ADD COMMENTlink written 7 months ago by Jennifer Hillman Jackson25k
0
gravatar for luisafermercadom
7 months ago by
luisafermercadom0 wrote:

Thank you,

I could easily separate the multi-mapped reads using NGS: BamTools > Filter BAM datasets on a variety of attributes

ADD COMMENTlink written 7 months ago by luisafermercadom0
0
gravatar for sf.rocha
6 days ago by
sf.rocha0
sf.rocha0 wrote:

I'm having issues with using the NGS: BamTools > Filter BAM datasets on a variety of attributes. I'm using as input a BAM file obtained with HISAT2 and I want to filter for only the reads that have only 1 mapping hit. For this I filtered on: Select BAM property to filter on > tag Filter on a particular tag > NH:=1

In the 'filtered bam' output file I get this as a summary: { "filters": [ { "tag": "NH:=1", "id": "1" } ] }

and if I visualize the data by clicking on the 'eye' icon, I only have the header.

Am I doing anything wrong?

ADD COMMENTlink written 6 days ago by sf.rocha0

Hi - Use this term instead: NH:1

Thanks! Jen, Galaxy team

ADD REPLYlink written 6 days ago by Jennifer Hillman Jackson25k
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