Keren Zhou

add an argument for bamtocov to allow the extension of reads to fragment size from single-end sequencing data

4

**Is your feature request related to a problem? Please describe.** In most of the IP-based methods, we need to extend reads to the fragment size to get the correct coverage...

How did bamtocov deal with paired-end bam from stranded libraries?

1

@telatin Dear Dr. Telatin, I'm curious about how `bamtocov` deal with paired-end bam from stranded libraries by setting with `--stranded`. Will `bamtocov` automatically treat mated reads as reverse strand? For...

intervene venn doesn't work with "--bedtools-option s=True"

2

Can intervene be complemented with "bedtools intersect -s "? (that is intersecting peaks by strand)

running enrichGO() function on MSigDB gene set

2

Hi YuLab members, Are there any ways to run enrichGO() function on MSigDB gene set (like HALLMARK gene set)? Best, Keren

How to generate data_repo for hg38 genome?

17

After calling CNVs by ReadDepth (reads mapped to hg38), I tried to get seed intervals by running `amplified_intervals.py`. But I got errors as bellow (run program on a HPC server):...

As in the title, are the coordinates in *_cycles.txt in 1-based format?

How to interpret results like "Segments=0+,12+,0-"?

6

Hi Jens, How to interpret results like "Segments=0+,12+,0-"? There is only one segment in this cycle. Best, Keren

How to interpret results like "Segments=13+,83-,105+,139-,0-,0+"?

1

Hi Jens, After running AmpliconArchitect, I got results like following: Cycle=66;Copy_count=0.0929550935359;Segments=13+,83-,105+,139-,0-,0+. I don't know how to interpret this result. Could you please do me a favor? Best, Keren

Hi Josie, I'm wondering that whether I can obtain the reads counts for gene by directly mapping reads to sequence from the whole gene locus instead of transcripts (minimap2 -ax...