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Forum: Bioinformatics 04-21-2016, 02:38 PM
Replies: 3
Views: 1,257
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: 827
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: 540
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: 1,113
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: [email protected]

...
Forum: Bioinformatics 01-11-2016, 09:42 AM
Replies: 2
Views: 793
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: 629
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: 1,004
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: 2,750
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: 855
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: 21,140
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: 21,140
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: 761
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: 2,156
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: 1,317
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: 8,218
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: 1,638
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: 2,465
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: 803
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: 1,635
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: 1,635
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: 814
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: 670
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: 1,311
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: 1,311
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...
Forum: Bioinformatics 02-11-2014, 11:56 AM
Replies: 3
Views: 2,377
Posted By m_two
Look here: http://www.biostars.org/p/13807/ ...

Look here: http://www.biostars.org/p/13807/

Breakdancer and Pindel will not really work because most breakpoints are not captured by exome capture sequencing. You will need an approach based on...
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