User: tbb21

gravatar for tbb21
tbb210
Reputation:
0
Status:
New User
Last seen:
1 week ago
Joined:
1 month, 1 week ago
Email:
t****@duke.edu

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

This helps us discourage the inappropriate use of our site.

Posts by tbb21

<prev • 9 results • page 1 of 1 • next >
0
votes
1
answer
82
views
1
answer
I16 Info Tag
... Hi all, bioinformatics noob here. I have been trying to call variants and don't fully understand what the I16 tag's first 4 entries mean. I found this table: 1 #reference Q13 bases on the forward strand 2 #reference Q13 bases on the reverse strand 3 #non-ref Q13 bases on the forward stra ...
bcftools snp mpileup sequencing written 7 days ago by tbb210 • updated 6 days ago by finswimmer8.0k
0
votes
0
answers
551
views
0
answers
Comment: C: Changing samtools mpileup I16 calculations?
... This is a great question I would also love the answer to. ...
written 7 days ago by tbb210
0
votes
0
answers
1.4k
views
0
answers
Comment: C: VCF/BCF File format QS score in INFO header
... I have the exact same question. Can't find an answer anywhere and have no idea why this hasn't been answered! ...
written 7 days ago by tbb210
0
votes
0
answers
118
views
0
answers
Comment: C: Filtering Read Quality - Cant remove all reads that have a single base below a t
... Thanks re the gold standard and I have now saved and uploaded all of the relevant plots! ...
written 7 days ago by tbb210
0
votes
0
answers
118
views
0
answers
Comment: C: Filtering Read Quality - Cant remove all reads that have a single base below a t
... Sorry its a single base. I have corrected this. ...
written 7 days ago by tbb210
0
votes
2
answers
1.7k
views
2
answers
Comment: C: What does <*> mean in a vcf file?
... Upon a second reading I think it may be a wildcard placeholder for any other alternative allele? So if I have an output like this: A (REF) G,<*> (ALT) and the PL is: 0,57,255,78,255,255. So does this mean that the PLs correspond to: AA, AG, GG, A<*>, G<*>, <*><*>? ...
written 7 days ago by tbb210
0
votes
0
answers
118
views
0
answers
Filtering Read Quality - Cant remove all reads that have a single base below a threshold
... Hi Biostars, I am new to handling sequencing data so this is my first time posting here! So I am trying to remove all reads with any of their base pairs below a threshold quality score, here 32. I have tried using the FASTQ quality_filter using `fastq_quality_filter -q 32 -p 100 -o output.fastq.g ...
filter fastx quality-score sequencing written 7 days ago by tbb210
0
votes
1
answer
3.3k
views
1
answers
Comment: C: Fastq Quality Filter Parameters
... Can you give any comments on what the gold standard is. For example, all reads needing to be above a Phred score of 32? ...
written 7 days ago by tbb210
0
votes
2
answers
1.7k
views
2
answers
Comment: C: What does <*> mean in a vcf file?
... Sorry but can you please explain what you mean by homozygous reference sites in this context? ...
written 8 days ago by tbb210

Latest awards to tbb21

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: 800 users visited in the last hour