User: adampennycuick

gravatar for adampennycuick
Reputation:
110
Status:
Trusted
Location:
UCL, London
Last seen:
6 days, 14 hours ago
Joined:
9 months ago
Email:
a*************@gmail.com

Posts by adampennycuick

<prev • 8 results • page 1 of 1 • next >
4
votes
1
answer
263
views
5 follow
1
answer
Cox proportional hazards - how to interpret summary output
... Hi all, I've been using a cox proportional hazard model to do survival analysis in R. I am looking for some advice interpreting the p-values produced by this model. I came across the interesting case where I stratified my data into two groups and the survival curve looked like this: ![Survival cur ...
R written 9 weeks ago by adampennycuick110 • updated 8 weeks ago by Biostar ♦♦ 20
0
votes
1
answer
501
views
1
answers
Comment: C: TCGA calling pipeline query
... Thanks both. Mathias - that link was very helpful (and hard to find!) - from reading this I think the discrepancy is that the openly accessible files I am using are masked MAF files, which don't contain all mutations, as germline mutations are masked. So to replicate their results I think I'd have t ...
written 8 months ago by adampennycuick110
5
votes
1
answer
501
views
6 follow
1
answer
TCGA calling pipeline query
... Hi all, I am trying to download mutation data from the TCGA LUSC project. My goal is to be able to programmatically calculate the mutation rate in this cohort for a given gene (e.g. TP53). Using the (excellent) online browser at https://portal.gdc.cancer.gov and selecting only the LUSC project, I ...
tcga written 8 months ago by adampennycuick110 • updated 8 months ago by badredda50
0
votes
3
answers
1.2k
views
3
answers
Comment: C: Converting BAM to Fastq - losing reads
... I think you have cracked it - the supplementary alignments are being lost. However, I don't think this is the behaviour that I want. These are DNAseq reads aligned using bwa mem. I want to extract ALL reads to fastq and realign to a new reference genome. As I understand it, supplementary reads may ...
written 8 months ago by adampennycuick110
0
votes
3
answers
1.2k
views
3
answers
Comment: C: Converting BAM to Fastq - losing reads
... Thanks but I don't think this is it - there are no secondary alignments identified by samtools flagstat ...
written 9 months ago by adampennycuick110
0
votes
3
answers
1.2k
views
3
answers
Comment: C: Converting BAM to Fastq - losing reads
... Good thought. The output is below for one of the coordinates which gives an error, for a sorted file. I am not great at interpreting these data, but perhaps the problem here is that there are an odd number of reads mapping to these coordinates so they cannot be appropriately paired? Do you know how ...
written 9 months ago by adampennycuick110 • updated 9 months ago by genomax59k
0
votes
3
answers
1.2k
views
3
answers
Comment: C: Converting BAM to Fastq - losing reads
... Thanks Devon, but that's not it. When I add the -s option it returns an empty file. And this doesn't explain the behaviour of bamToFastq. ...
written 9 months ago by adampennycuick110
12
votes
3
answers
1.2k
views
11 follow
3
answers
Converting BAM to Fastq - losing reads
... Hi all, I am trying to realign a whole genome BAM file from one reference genome to another. The reason for this is that I am interested in HLA regions, and the original reference genome does not include these regions. The process involves converting the name-sorted BAM file to fastq, then realigni ...
alignment written 9 months ago by adampennycuick110 • updated 8 months ago by h.mon21k

Latest awards to adampennycuick

Popular Question 6 weeks ago, created a question with more than 1,000 views. For Converting BAM to Fastq - losing reads
Student 8 months ago, asked a question with at least 3 up-votes. For TCGA calling pipeline query
Student 9 months ago, asked a question with at least 3 up-votes. For Converting BAM to Fastq - losing reads

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1026 users visited in the last hour