Ryan Layer

Thanks for the suggestion John! On Wed, Apr 21, 2021 at 6:03 AM John Marshall ***@***.***> wrote: > Just remove -lcrypto in *src/filter/Makefile*, and run make again. HTSlib > does...

This is typically either a python issue or that your system does not have hexdump. See https://github.com/arq5x/lumpy-sv/issues/256 I would recommend using the latest lumpy wrapper, smoove. https://github.com/brentp/smoove On Mon, May...

It really depends on your experiment, but I typically filter SVs that are larger than 1MB. Try visualizing your SVs with samplot. For big SVs use the —zoom 500 option....

Yep. Those big SVs are usually repeat artifacts that can be difficult to remove. Lumpy takes an exclude region file that you can add to I’d you want. We typically...

Yep. looks good. On Fri, Feb 14, 2020 at 9:25 AM Limitto wrote: > Can you elaborate on how do you "subtract SVs with repeat tracks"? > > I was...

pairend_distro.py needs at least 1000 alignments to determine the stats that lumpy uses to id breakpoints. These alignments must: have the flags "read paired", "mast reverse strand", "first in pair"...

Can you check to see what the flags and insert sizes are on the first 1M records? On Tue, Aug 23, 2016 at 1:59 PM, Stanley Chin [email protected] wrote: >...

Can you send me a bam with the first 1M alignments? On Wed, Aug 24, 2016 at 11:15 AM, Stanley Chin [email protected] wrote: > Here are some examples of reads...

Gmail, ryan dot layer > On Aug 26, 2016, at 9:01 AM, Stanley Chin [email protected] wrote: > > Hi Ryan, what is your email? I can't seem to find it...

Can you rerun with the verbose flag on (-v) and reply with the output? On Tue, Nov 8, 2016 at 9:16 AM, aderzelle [email protected] wrote: > Hello, > I am...