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Forum: Bioinformatics 05-20-2016, 04:48 AM
Replies: 2
Views: 1,701
Posted By maxsalm
Hi there, personally I have had success with...

Hi there,

personally I have had success with BWA/BWA-MEM followed by Picard's MarkDuplicates. N.B. It is important to align to the FULL genome (not just canonical chromosomes).
Forum: Bioinformatics 02-26-2016, 04:40 AM
Replies: 4
Views: 2,668
Posted By maxsalm
I can highly recommend Ruffus...

I can highly recommend Ruffus http://www.ruffus.org.uk/
Forum: Bioinformatics 01-05-2016, 01:19 AM
Replies: 0
Views: 835
Posted By maxsalm
Depsy: Software credit

Hi everyone,

I just came across this wonderful resource, whose metrics may bolster grant applications.

http://depsy.org/
Forum: Bioinformatics 12-04-2015, 05:14 AM
Replies: 2
Views: 1,057
Posted By maxsalm
Hi there, for the mapping part, you could try...

Hi there, for the mapping part, you could try Stampy (http://www.well.ox.ac.uk/project-stampy) or BBMap (http://sourceforge.net/projects/bbmap/) which can accommodate greater sequence divergence.
Forum: Bioinformatics 12-04-2015, 05:02 AM
Replies: 4
Views: 1,794
Posted By maxsalm
Hi there! You could try the CORTEX assembler:...

Hi there! You could try the CORTEX assembler: http://www.ncbi.nlm.nih.gov/pubmed/23172865
Forum: Bioinformatics 10-23-2015, 04:37 AM
Replies: 4
Views: 1,843
Posted By maxsalm
Hi there! You may also find mRIN useful:...

Hi there! You may also find mRIN useful: http://www.ncbi.nlm.nih.gov/pubmed/26234653
Forum: Bioinformatics 10-09-2015, 04:40 AM
Replies: 12
Views: 4,768
Posted By maxsalm
Hi there! I would take a look at this...

Hi there!

I would take a look at this excellent review to help with your coverage requirements:
http://www.nature.com/nrg/journal/v15/n2/full/nrg3642.html
Forum: Bioinformatics 07-03-2015, 05:25 AM
Replies: 6
Views: 1,485
Posted By maxsalm
FastQC may also be of general use:...

FastQC may also be of general use: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Forum: Bioinformatics 07-03-2015, 05:19 AM
Replies: 2
Views: 2,433
Posted By maxsalm
Hi there, I believe that function has been...

Hi there,

I believe that function has been deprecated, and been replaced with readGAlignmentsFromBam() - see here for more details: https://support.bioconductor.org/p/61854/
Forum: Bioinformatics 06-22-2015, 02:10 AM
Replies: 7
Views: 3,939
Posted By maxsalm
Another option may be to get in touch with the...

Another option may be to get in touch with the Snyder lab and study the same transcriptomes used in their exploration of PacBio long-reads:
...
Forum: Bioinformatics 06-22-2015, 01:59 AM
Replies: 1
Views: 829
Posted By maxsalm
There are hundreds, depending on your field of...

There are hundreds, depending on your field of interest! Some key sites are:
http://www.cbioportal.org/
http://www.intogen.org/search
http://cancer.sanger.ac.uk/cosmic ...
Forum: Bioinformatics 05-08-2015, 06:18 AM
Replies: 1
Views: 895
Posted By maxsalm
Hi there, if you can transform your data...

Hi there,

if you can transform your data into BED format, you might have some luck with "closest" tool in BEDtools (http://bedtools.readthedocs.org/en/latest/). Good luck!
Forum: Bioinformatics 04-24-2015, 04:06 AM
Replies: 6
Views: 1,605
Posted By maxsalm
This is also a great tutorial:...

This is also a great tutorial: http://arxiv.org/abs/1302.3685
Forum: Core Facilities 04-10-2015, 05:24 AM
Replies: 0
Views: 2,866
Posted By maxsalm
Core services: Reward bioinformaticians

Hi everyone!

Although I'm definitely biased in this regard, I highly recommend a read of this timely commentary in Nature:
http://www.nature.com/news/core-services-reward-bioinformaticians-1.17251
Forum: Bioinformatics 03-27-2015, 05:47 AM
Replies: 28
Views: 60,134
Posted By maxsalm
Hi everyone, the ever impressive bedtools...

Hi everyone,

the ever impressive bedtools also has a BAM-to-FASTQ utility ( http://bedtools.readthedocs.org/en/latest/content/tools/bamtofastq.html )
Forum: Genomic Resequencing 03-17-2015, 02:59 AM
Replies: 4
Views: 2,582
Posted By maxsalm
Personally, I always keep the BAM files till the...

Personally, I always keep the BAM files till the end of the analysis: nearly all of the CNV calling methods I've tried use these as a starting point anyway, so this offers you some flexibility to try...
Forum: Genomic Resequencing 03-17-2015, 02:33 AM
Replies: 4
Views: 2,582
Posted By maxsalm
Hi there, a lot of approaches have already been...

Hi there,
a lot of approaches have already been developed for calling CNVs from Illumina data, and are tailored to different sources of data (WGS, WES, etc.). A good overview can be found here:...
Forum: Bioinformatics 02-27-2015, 04:50 AM
Replies: 18
Views: 5,934
Posted By maxsalm
You may also find Scalpel useful...

You may also find Scalpel useful (http://scalpel.sourceforge.net/) which uses an assembly step during indel calling (http://www.ncbi.nlm.nih.gov/pubmed/25128977 ) that may help with some of the...
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