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Forum: Bioinformatics 02-25-2020, 06:42 AM
Replies: 1
Views: 719
Posted By m_two
The PAR is typically masked on chrY since the PAR...

The PAR is typically masked on chrY since the PAR reference is an exact duplicate of chrX sequence.

chrY unique regions tend to be repetitive and highly variable with many deletions, duplications,...
Forum: Bioinformatics 04-21-2016, 02:38 PM
Replies: 3
Views: 1,917
Posted By m_two
The same aliquot may have been sequenced multiple...

The same aliquot may have been sequenced multiple times and/or processed multiple times:

Some aliquots have been sequenced for VALIDATION, WGS, and WXS
Some aliquots have been captured with...
Forum: Bioinformatics 03-15-2016, 10:16 AM
Replies: 3
Views: 1,150
Posted By m_two
see https://www.biostars.org/p/66843/

see https://www.biostars.org/p/66843/
Forum: Bioinformatics 02-23-2016, 10:12 AM
Replies: 1
orf
Views: 799
Posted By m_two
I would review the Ensembl documentation...

I would review the Ensembl documentation regarding the Transcript Support Level (TSL)

ensembl.org/Help/Glossary?id=492

This may be a helpful publication...
Forum: Bioinformatics 02-02-2016, 07:54 AM
Replies: 10
Views: 1,603
Posted By m_two
Primer-blast Link:...

Primer-blast

Link: http://www.ncbi.nlm.nih.gov/tools/primer-blast/
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastNews#13
Contact: blast-help@ncbi.nlm.nih.gov

...
Forum: Bioinformatics 01-11-2016, 09:42 AM
Replies: 2
Views: 1,194
Posted By m_two
http://bioinformatics.mdanderson.org/main/Transvar...

http://bioinformatics.mdanderson.org/main/Transvar

Introduction

TransVar is a reverse annotator for inferring genomic characterization(s) of mutations (e.g., chr3:178936091 G/A) from protein or...
Forum: Bioinformatics 01-04-2016, 10:51 AM
Replies: 2
Views: 949
Posted By m_two
You might also try clinvar: ...

You might also try clinvar:

http://www.ncbi.nlm.nih.gov/clinvar/?term=BRCA1
Forum: Bioinformatics 12-29-2015, 09:58 AM
Replies: 4
Views: 1,531
Posted By m_two
What software produced the output? Does the...

What software produced the output?

Does the meta-information line match this?
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">

If the vcf metainfo matches the line below refer...
Forum: Bioinformatics 12-29-2015, 08:10 AM
Replies: 2
Views: 4,259
Posted By m_two
Before obtaining and reprocessing the sequence...

Before obtaining and reprocessing the sequence data on your own I would review the freely available and open access processed data.

* https://wiki.nci.nih.gov/display/TCGA/RNASeq+Version+2 -...
Forum: Bioinformatics 07-27-2015, 02:47 PM
Replies: 11
Views: 1,216
Posted By m_two
Check out bedtools: ...

Check out bedtools:

http://bedtools.readthedocs.org/en/latest/content/tools/intersect.html

ExAc may also be a better source of rare germline SNPs in coding regions
...
Forum: Bioinformatics 07-27-2015, 02:34 PM
Replies: 14
Views: 22,741
Posted By m_two
dbSNP data is available in VCF format on FTP and...

dbSNP data is available in VCF format on FTP and pretty well documented but not as extensive or up-to-date as ExAc. It never hurts to have a backup.

...
Forum: Bioinformatics 07-27-2015, 02:25 PM
Replies: 14
Views: 22,741
Posted By m_two
Consider using Exac to identify germline SNPs in...

Consider using Exac to identify germline SNPs in coding regions.

The Jan 2015 release consolidates exomes data from 60,706 individuals.

http://exac.broadinstitute.org/
...
Forum: Bioinformatics 06-15-2015, 07:44 AM
Replies: 2
Views: 953
Posted By m_two
If you concatenate the forward and reverse...

If you concatenate the forward and reverse complement of the reverse primer sequence into a single sequence then this blast command should return all possible products up to 2kb in size. Adjust...
Forum: Bioinformatics 03-30-2015, 08:12 AM
Replies: 2
Views: 2,771
Posted By m_two
You can download clinical data collected by the...

You can download clinical data collected by the BCR using the DAM:

https://tcga-data.nci.nih.gov/tcga/dataAccessMatrix.htm?

If you enter any "disease code" you can find all open access BCR data...
Forum: Bioinformatics 11-03-2014, 11:57 AM
Replies: 3
Views: 1,731
Posted By m_two
1000 Genomes FTP site has some recent data ...

1000 Genomes FTP site has some recent data

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20140123_NA12878_Illumina_Platinum
...
Forum: Bioinformatics 10-29-2014, 07:43 AM
Replies: 12
Views: 9,751
Posted By m_two
Ensembl VEP is a best bet for custom annotation...

Ensembl VEP is a best bet for custom annotation (fast, robust, reliable, and easily automated)

http://useast.ensembl.org/info/docs/tools/vep/script/vep_custom.html...
Forum: Bioinformatics 06-04-2014, 03:13 PM
Replies: 2
Views: 1,902
Posted By m_two
Based on this result...

Based on this result https://www.synapse.org/#!Synapse:syn312572/wiki/63089

I would consider adding Delly since Novobreak has not been released yet. Sensitivity is still an issue. Given the...
Forum: Bioinformatics 05-14-2014, 08:32 AM
Replies: 10
Views: 3,014
Posted By m_two
These lolliplots/mutation diagrams required...

These lolliplots/mutation diagrams required minimal touch up:
http://www.nature.com/ncomms/2014/140122/ncomms4156/fig_tab/ncomms4156_F3.html

They originated from:...
Forum: Bioinformatics 04-29-2014, 02:38 PM
Replies: 1
Views: 1,106
Posted By m_two
Q: What would you consider the lowest reasonable...

Q: What would you consider the lowest reasonable Allele frequency for a heterozygous germline SNP. Something like between 30% and 60% ?

It's a dependent on the of coverage of that site. If...
Forum: Bioinformatics 03-27-2014, 01:27 PM
Replies: 4
Views: 1,883
Posted By m_two
Related: Global optimization of somatic...

Related:

Global optimization of somatic variant identification in cancer genomes with a global community challenge
http://www.nature.com/ng/journal/v46/n4/full/ng.2932.html
Forum: Bioinformatics 03-13-2014, 08:55 AM
Replies: 4
Views: 1,883
Posted By m_two
Comparing somatic mutation-callers: beyond Venn...

Comparing somatic mutation-callers: beyond Venn diagrams
Su Yeon Kim and Terence P Speed
http://www.biomedcentral.com/1471-2105/14/189
Forum: Bioinformatics 03-05-2014, 02:19 PM
Replies: 2
Views: 1,109
Posted By m_two
Try Tigra-SV ...

Try Tigra-SV

http://gmt.genome.wustl.edu/tigra-sv/0.1/index.html
http://genome.cshlp.org/content/24/2/310
Forum: Bioinformatics 02-26-2014, 06:45 AM
Replies: 1
Views: 845
Posted By m_two
Use Ensembl: ...

Use Ensembl:

http://useast.ensembl.org/info/genome/compara/homology_method.html

Search there FAQs to find exactly what you are looking for:

http://goo.gl/FQQqsF
Forum: Bioinformatics 02-11-2014, 12:35 PM
Replies: 2
Views: 1,838
Posted By m_two
In addition, this may be useful:...

In addition, this may be useful: http://evs.gs.washington.edu/EVS/
Forum: Bioinformatics 02-11-2014, 12:34 PM
Replies: 2
Views: 1,838
Posted By m_two
You may want to download the dbSNP VCF file...

You may want to download the dbSNP VCF file containing the 1000 Genome's project minor allele frequencies.
ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/

You can use joinx to process...
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