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t-neumann / slamdunk

Streamlining SLAM-seq analysis with ultra-high sensitivity
GNU Affero General Public License v3.0
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Genomic locations of the TC reads #122

Closed aishwarya-gondane closed 1 year ago

aishwarya-gondane commented 1 year ago

Hi,

I was wondering if it is possible to fish out the exact genomic locations of the TC reads. For example, the transcript length is 800 bp and has 50 TCReadCount. Is it possible to know the exact location of these TCReads?

t-neumann commented 1 year ago

what you could do is use the alleyoop read-separator script that gives you separate bam files for labelled and unlabelled reads and you could take it from there

aishwarya-gondane commented 1 year ago

Hi Tobias,

Thanks for the suggestion. I have used the alleyoop read-separator module to get the TC Filtered BAM files and then converted them to bed files to look at the genomic locations. Is this the correct approach?

t-neumann commented 1 year ago

Yupp sounds good to me