User: QPaps04

gravatar for QPaps04
QPaps040
Reputation:
0
Status:
New User
Last seen:
3 days, 7 hours ago
Joined:
1 year, 4 months ago
Email:
e**********@hotmail.co.uk

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

This helps us discourage the inappropriate use of our site.

Posts by QPaps04

<prev • 14 results • page 1 of 2 • next >
0
votes
1
answer
209
views
1
answers
Answer: A: segmentation fault in Bayenv2
... I have also come across this error and the only answer I found lies in the realms of [twitter][1] -thanks @craigandersn! Although I have asked for clarification on what he means. It is something to do with the population names not being sequential. I hope this helps and if you can help me understan ...
written 4 days ago by QPaps040
0
votes
0
answers
32
views
0
answers
Deeptools plotCoverage and bamPEFragmentSize change axes
... Hello all, I am using `deeptools 3.5.0` I have successfully run both `plotCoverage` and `bamPEFragmentSize` on my `.bam` file and it has output the plots. However, is there a way to change the **limits of the x and y-axis**? My apologies if there is a simple solution. I am new to these types of ...
deeptools next-gen coverage snp sequencing written 5 days ago by QPaps040
0
votes
1
answer
2.2k
views
1
answers
Answer: A: VCFTools error: Unrecognized values used for CHROM, Replacing with 0.
... Hello, I know this is a very old post but I have just been trying to solve this exact problem. I have a genome that is made up of lots of scaffolds (not a model organism) and so I recieved the error message you report for all my scaffolds. I found the solution by following this tutorial [http://ev ...
written 18 days ago by QPaps040
0
votes
1
answer
233
views
1
answer
Alternative to PGDSpider for vcf conversion
... Hello all, I have been trying to convert a large `vcf` file to `GESTE_BAYE_SCAN` format using PGDSpider. I have tried doing a straight conversion and also a two-step: `vcf > PGD > GEST_BAYE_SCAN`. The first step works. Hoever every time I try to produce the BayeScn file I get this error: `ERRO ...
vcf next-gen snp conversion memory written 4 months ago by QPaps040 • updated 25 days ago by jpr6mg0
1
vote
1
answer
179
views
1
answers
Answer: A: remove listed singletons from vcftools output
... If anyone is having a similar problem - I found the solution! Instead of using `--exclude` flag use the `--exclude-positions` flag for `vcftools`. Make sure you take the 1st and second column of the `--singletons` output. ...
written 4 months ago by QPaps040
1
vote
1
answer
179
views
1
answer
remove listed singletons from vcftools output
... Hello all, I would like to remove any singletons/doubletons from my vcf file. I can find all the singletons/doubletons using: `vcftools --vcf file.vcf --singletons --out file` This output `file.singletons` which has this information: `CHROM POS SINGLETON/DOUBLETON ALLELE INDV` I thou ...
genome next-gen vcftools sequencing written 4 months ago by QPaps040
0
votes
0
answers
146
views
0
answers
Comment: C: Filter SNPs for DP using mean + 2*SD
... If not - how would you set the maximum depth allowance - so its not just an arbitary number? Thank you for your advice ...
written 5 months ago by QPaps040
0
votes
0
answers
146
views
0
answers
Comment: C: Filter SNPs for DP using mean + 2*SD
... I see, but this would be controlled for by filtering using `-minDP`? ...
written 5 months ago by QPaps040
0
votes
0
answers
146
views
0
answers
Filter SNPs for DP using mean + 2*SD
... Hello all, I am trying to filter a SNP file (.vcf) for max depth. Instead of choosing a random number it has been suggested that I could use the `mean + (2*SD)` as a limit for the amount of depth allowed. Does anyone know how to carry this out using `vcftools` or the alike? I know I can filter usi ...
filter next-gen vcftools snp depth written 5 months ago by QPaps040
0
votes
0
answers
1.6k
views
0
answers
Comment: C: how to estimate mean and standard deviation read depth for all the variants?
... Sorry to open a very old chain. I am also trying to find a way to do this. However, I also got the same output (i.e. 0 0) as @reza? @reza did you ever find a method to do this? Thanks ...
written 5 months ago by QPaps040

Latest awards to QPaps04

Scholar 4 months ago, created an answer that has been accepted. For A: remove listed singletons from vcftools output

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1541 users visited in the last hour