User: amna.farooq

gravatar for amna.farooq
Reputation:
0
Status:
New User
Last seen:
3 years, 2 months ago
Joined:
3 years, 4 months ago
Email:
a**********@bs.qau.edu.pk

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by amna.farooq

<prev • 4 results • page 1 of 1 • next >
0
votes
0
answers
852
views
0
answers
Comment: C: calculating conservation depth of multiple regions(in form of bed coordinates)
... nopes.... not per base, i think thats the main issue. phyloP and PhastCons both give me per base score, but i need to estimate conservation depth of whole patch/region. very crude solution was to average the per base score of whole region to get one mean score of whole region, but thats not working, ...
written 3.2 years ago by amna.farooq0
0
votes
0
answers
852
views
0
answers
Comment: C: calculating conservation depth of multiple regions(in form of bed coordinates)
... an other solution i saw was to check for the maximum distant specie having at least 50% sequence conserved with query sequence in chain file. but when i see chain files on ucsc, they are splited into blocks or patches according to conservation . i cant understand how to combine those blocks to searc ...
written 3.3 years ago by amna.farooq0
0
votes
0
answers
852
views
0
answers
calculating conservation depth of multiple regions(in form of bed coordinates)
... hello! i am trying to calculate conservation depth of multiple regions (100-3000 bps) present in human genome. since regions are more than 10,000, its not possible to check conservation manually. i attempted to download phastcons score files from ucsc (46way.wigifx files). and when i tried to averag ...
0
votes
1
answer
4.7k
views
1
answers
Comment: C: Measuring Conservation For Short Motif
... great effort lan ! i used it and found interesting. but do you think mean and max phast score would work if we need to find conservastion of bit longer regions , say 500-3000 bps? chr7:21114483-21117423 (hg19) has phastcons max =1 and mean= 0.437672 when i check it in UCSC browser, its conserved dow ...
written 3.3 years ago by amna.farooq0

Latest awards to amna.farooq

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1378 users visited in the last hour