User: aalith

gravatar for aalith
aalith10
Reputation:
10
Status:
New User
Location:
Last seen:
9 months, 1 week ago
Joined:
11 months, 4 weeks ago
Email:
a*****@hotmail.com

Posts by aalith

<prev • 27 results • page 1 of 3 • next >
0
votes
1
answer
504
views
1
answer
Difference between Pysam Pileup and Fetch
... I've been attempting to use pysam to find how many reads support a particular SNP vs how many reads do not. I have not been able to exactly pinpoint what pysam pileup is doing. Is it exactly like the samtools function? For example, to compare what exactly is focused on for each function, I've run ...
reads bam pysam pileup written 9 months ago by aalith10 • updated 7 months ago by castaway19900
0
votes
0
answers
223
views
0
answers
Reducing block size used in Spark versions of GATK tools
... Hi all, I've been attempting to run GATK's MarkDuplicatesSpark on a bam file that's about 160G, however, I keep getting errors about running out of space on my device. I've allotted Docker 850G of space, which should be enough in my mind. The following command takes around 2 days to reach an error. ...
gatk dna block size spark written 9 months ago by aalith10 • updated 9 months ago by Biostar ♦♦ 20
0
votes
0
answers
411
views
0
answers
Comment: C: GATK MarkDuplicatesSpark Space Issues
... Thanks! That post is helpful, but I'm new to docker... how would I implement this in docker? I may fall back to the regular MarkDuplicates! I'd just need to sort by queryname first ...
written 10 months ago by aalith10
0
votes
0
answers
411
views
0
answers
Comment: C: GATK MarkDuplicatesSpark Space Issues
... That's what I thought, but does this make sense? I need more than 850 gigs allocated to Docker? ...
written 10 months ago by aalith10
0
votes
0
answers
411
views
0
answers
GATK MarkDuplicatesSpark Space Issues
... I'm using GATK's function to mark PCR duplicates in my bam files before running through base quality score recalibration then MuTect. My bam file is 166G. I keep getting errors about space, but I am running nothing else on Docker concurrently. I have given Docker 14 cores, 850G of storage, and 55G ...
gatk markduplicates written 10 months ago by aalith10
0
votes
1
answer
360
views
1
answers
Comment: C: Finding # of UMIs with and without specific SNP
... Sorry for editing this so much, but having another bit of trouble.. To see the nucleotide at the specific point of interest, I did the following - subset to only chromosome 3 at position 50093871 (for reads in bamfile.fetch('3', 50093871, 50093872)) - Find the specific nucleotide by reads.seq[5009 ...
written 11 months ago by aalith10
0
votes
1
answer
360
views
1
answers
Comment: C: Finding # of UMIs with and without specific SNP
... So I'll have to use *fetch* instead of pileup so i can hold on to the tags? ...
written 11 months ago by aalith10
0
votes
1
answer
360
views
1
answers
Comment: C: Finding # of UMIs with and without specific SNP
... this is unbelievably helpful, thank you! ...
written 11 months ago by aalith10
0
votes
1
answer
360
views
1
answers
Comment: C: Finding # of UMIs with and without specific SNP
... Sorry for being unclear - I am trying to count the number of UMIs associated with reads that contain a particular SNP. So, count the number of different UMIs associated with reads that do and do not contain the SNP ...
written 11 months ago by aalith10
0
votes
1
answer
360
views
1
answers
Comment: C: Finding # of UMIs with and without specific SNP
... UMIs are currently denoted by the XM tag in my bam file ...
written 11 months ago by aalith10

Latest awards to aalith

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: 1168 users visited in the last hour