User: yryan

gravatar for yryan
yryan0
Reputation:
0
Status:
New User
Last seen:
5 months, 3 weeks ago
Joined:
1 year, 5 months ago
Email:
y****@liv.ac.uk

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

This helps us discourage the inappropriate use of our site.

Posts by yryan

<prev • 16 results • page 1 of 2 • next >
0
votes
0
answers
211
views
0
answers
Salmon validating best settings for use case
... Hi folks, I've got some illumina based mouse transcriptomic data. I've done multiple runs with salmon so I can compare the effects of cDNA, to partial and full selective alignment with decoys for indexes. I'm also repeating each of those with --gcBias and --seqBias on and off. However moving forw ...
salmon rna-seq validation written 8 months ago by yryan0
0
votes
1
answer
200
views
1
answers
Comment: C: Can you use salmon bootstraps to increase sample size for machine learning
... Okay, thanks! (making up characters to comment) ...
written 8 months ago by yryan0
1
vote
1
answer
200
views
1
answer
Can you use salmon bootstraps to increase sample size for machine learning
... Hi folks, I've got some time course matched RNA seq experiments with n=6 for controls and exposures. I'm trying to do some machine learning classification with these. I'm wondering if using the bootstraps generated by salmon is a valid way of increasing my sample size or is this not really suitable ...
salmon machine learning rna-seq written 8 months ago by yryan0 • updated 8 months ago by ATpoint44k
0
votes
0
answers
408
views
0
answers
Pysam get query sequence range without loop
... Hi folks, I'm trying to optimise my code here. Esentially I'm trying to use pysam to get a list of bases of reads around a base of interest as shown in the code below. However my code is quite inefficient as the only way I've managed to get it working is by looping through each column in the pileup ...
python pysam written 11 months ago by yryan0
0
votes
0
answers
435
views
0
answers
Comment: C: Pysam pileup dropping reads
... I've found ` set_min_base_quality(self, min_base_quality)` and added that to my code on line 15 just after the else which now works perfectly. Thanks for helping point me in the right direction! ...
written 11 months ago by yryan0
0
votes
0
answers
435
views
0
answers
Comment: C: Pysam pileup dropping reads
... It gives me the same number that my `print("Total counted ", total)` line gives me. But in the docs it says : > This method applies a base quality filter and the number is equal to the size of get_query_sequences(), get_mapping_qualities(), etc. This makes me think its a quality score issue, I ...
written 11 months ago by yryan0
0
votes
0
answers
435
views
0
answers
Comment: C: Pysam pileup dropping reads
... Eyeballing it in a genomeviewer there are some deleted bases but looks do be much closer to 1 in 10 reads rather than 5-6/10 reads which my script is returning. I'm not sure if its a nanopore issue since it is only single reads and does have what looks to be many deletions but not enough over my reg ...
written 11 months ago by yryan0
0
votes
0
answers
435
views
0
answers
Pysam pileup dropping reads
... Hi folks, I'm trying to use pysam's pileup in order to count some base changes occurring at certain points in my transcript of interest using MinION data. However my coverage at each base is often three times as large as the total of reads in my final counts and I'm trying to figure out this discre ...
pysam pileup written 11 months ago by yryan0
0
votes
1
answer
288
views
1
answers
Comment: C: Modifying fastq base at specific reference location on different length reads
... I was wondering if I could get a bit more help... When I run the command `java -jar /bioinformatics_tools/jvarkit/dist/biostar404363.jar -o modified.bam -p basecalled.vcf original.bam ` The output is only partially converting all of my T's to N's for the first 30 or so entries, and the remainder ( ...
written 12 months ago by yryan0 • updated 12 months ago by GenoMax94k
0
votes
1
answer
652
views
1
answers
Comment: C: Is it possible to remove reads from BAM which match the reference at a position
... That worked perfectly, thanks so much for that! ...
written 12 months ago by yryan0

Latest awards to yryan

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: 1789 users visited in the last hour
_