Fahri Küçükali

icon indicating a website link https://uantwerpen.vib.be/member/37/Fahri_K%C3%BC%C3%A7%C3%BCkali icon indicating an email [email protected]

icon location Antwerp icon location Postdoctoral researcher at @SleegersLab-VIBCMN working on complex genetics of Alzheimer's. | GWAS, molecular QTLs, TWAS, splicing, long reads, rare variants.

Results 6 comments of Fahri Küçükali

Recalculating Rsq Imputation Quality Values

Hi Sayathan, thanks a lot for your answer, it is very clear! Indeed, mainly for rare variants I couldn't replicate the Rsq values I see in the imputation output VCFs....

Inconsistent Filtering of CIGAR Strings by filter_cs.py

Dear Yang, Thank you very much for explanation! I made a quick test on the same sample with this command: `regtools junctions extract -a 8 -m 50 -M 500000 $bamfile...

Inconsistent Filtering of CIGAR Strings by filter_cs.py

Hi again, I now have completed rerunning the sQTL mapping pipeline for regtools-quantified data, and compared it with the old data (that was quantified with old Leafcutter pipeline [bam2junc.sh]). I...

Inconsistent Filtering of CIGAR Strings by filter_cs.py

Dear Yang, Sorry for the delayed response, it has been a rather strange period of time! Indeed, I agree that the main step to be investigated should be the number...

Inconsistent Filtering of CIGAR Strings by filter_cs.py

Dear Yang, For a comprehensive comparison between the old and the new pipeline where you can also easily use the same files for further comparison/testing, I used the example GEUVADIS...

Inconsistent Filtering of CIGAR Strings by filter_cs.py

Dear Yang @goldenflaw (and other contributors), I made a new analysis; because, as I indicated in the above comment, I think the example test bam files provided in this repository...