Liang Lab at Brock University comments

Results 6 comments of


                                            Liang Lab at Brock University

Huge discrepancy in RepeatMasker lists between the UCSC version and the NCBI version

As an update, according to my analysis, the rmsk.bigBed version is missing some critical entries (e.g. full length L1s with full coding capacity).

Huge discrepancy in RepeatMasker lists between the UCSC version and the NCBI version

Here are the urls for the two files: http://t2t.gi.ucsc.edu/chm13/hub/t2t-chm13-v2.0/rmsk/rmsk.bigBed and https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_rm.out.gz. I like the UCSC version for having the chromosome number, but didn't expect to see that much of differences....

Huge discrepancy in RepeatMasker lists between the UCSC version and the NCBI version

Thank you Arrang for providing the new location of the data. However, the number of entries in chm13v2.0_rmsk.bb is even smaller (~900,000 less) than what's in rmsk.bigBed, unless I did...

Huge discrepancy in RepeatMasker lists between the UCSC version and the NCBI version

Hello, team! Thanks for looking into the issue. What I noticed is that with the same criteria, I found a total of 268 L1s that are young (low sequence divergence)...

Huge discrepancy in RepeatMasker lists between the UCSC version and the NCBI version

Hi Mark, If you missed my earlier post, what I found is that the huge discrepancies in number between the NCBI and UCSC RM list is due to the large...

vg augment forwardize_breakpoints error

I have the same issue, and when I tried to replace the vg input with the xg file, it says "Correct input type not found in grapeMC.xg while loading handlegraph::MutablePathMutableHandleGraph"