User: Duarte Molha

gravatar for Duarte Molha
Duarte Molha200
Reputation:
200
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Location:
Oxford, UK
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https://plus.google.co...
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Last seen:
7 months, 3 weeks ago
Joined:
6 years, 9 months ago
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about me

Posts by Duarte Molha

<prev • 35 results • page 1 of 4 • next >
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Comment: C: BWA.KIT where can i find it? Very confused
... Ok ... I think I got what is wrong. I downloaded what I thought was the latest version from that link (0.7.17 file) But the bwakit is the file below at version 0.7.15 Many thanks Feeling a bit of an idiot :) ...
written 7 months ago by Duarte Molha200
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Comment: C: BWA.KIT where can i find it? Very confused
... unfortunately this is not the case ,, take a look at the folder called doc and the resource-human-HLA. and the other resource folder none of those folders are on the downloads ... i know I checked ...
written 7 months ago by Duarte Molha200
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BWA.KIT where can i find it? Very confused
... Hi everyone I am thinking if testing the bwa.post processing for alt contigs provided by bwa.kit... but I am very confused BWA kit releases can be downloaded from here: https://sourceforge.net/projects/bio-bwa/files/bwakit and it seems it is hosted now on github here https://github.com/lh3/bwa/ ...
alt_mapping bwa bwakit written 7 months ago by Duarte Molha200 • updated 7 months ago by finswimmer11k
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Comment: C: BWA mem of a heavily masked reference index takes more time than the normal refe
... I think I understand your point... but why would BWA try to align any read against a string of N's? I can understand if it tried to align it against a homopolymer region and have some difficulty... but a homopolymer such as AAAA is a valid sequence to which you can try and find a alignment with a qu ...
written 12 months ago by Duarte Molha200
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Comment: C: BWA mem of a heavily masked reference index takes more time than the normal refe
... I know this to not be considered a good practice. But I was interested in looking at it anyway. As you can see in the my post I did consider the overfitting of the reads to my targets ... this is why I blated every partial match to my targets, expanded its length and kept those unmasked as well./ ...
written 12 months ago by Duarte Molha200
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BWA mem of a heavily masked reference index takes more time than the normal reference?
... Hi everyone I have a question regarding BWA mem alignment I was interested in finding out the performance gains I would obtain from creating a artificial reference where I masked everything I was not interested in my panel. In short I blated all my regions of interest on my panel and created a ma ...
alignment bwa written 12 months ago by Duarte Molha200 • updated 12 months ago by karl.stamm3.5k
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Comment: C: CNVkit : small CNV calling
... How did you reach that 20Kb value? would you mind sharing how you calculate that? ...
written 16 months ago by Duarte Molha200
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TGCA data download in latest assembly
... Hi guys I am interested in downloading data from the cancer genome atlas. All their data is available in MAF format and I will probably want to convert it to VCF. However before doing this I was wondering if anyone knows if there is anywhere I can obtain the data aligned to the latest assembly and ...
assembly tgca alignment data written 3.4 years ago by Duarte Molha200 • updated 3.4 years ago by Arnaud Ceol840
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Comment: C: How to visualise RNAseq baits in a genomic context
... I just used GMAP and it worked like a charm.. however @h.mon I do get a few baits that where the splice junction is very close to one of the extremities where the aligner will align that small chunk to the intronic region instead of the correct region on the other slice adjacent exon (see screenshot ...
written 4.1 years ago by Duarte Molha200
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Comment: C: How to visualise RNAseq baits in a genomic context
... Many thanks... I will try GMAP  ...
written 4.1 years ago by Duarte Molha200

Latest awards to Duarte Molha

Popular Question 14 months ago, created a question with more than 1,000 views. For How to visualise RNAseq baits in a genomic context
Epic Question 16 months ago, created a question with more than 10,000 views. For How Does Average Heterozygosity Relate To Alellic Frequency Data
Popular Question 2.5 years ago, created a question with more than 1,000 views. For 1000 Genomes Project Community Meeting
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Is It Possible To Filter Only Bookend Reads From A Bed File?
Great Question 3.3 years ago, created a question with more than 5,000 views. For How Does Average Heterozygosity Relate To Alellic Frequency Data
Popular Question 3.3 years ago, created a question with more than 1,000 views. For How Does Average Heterozygosity Relate To Alellic Frequency Data
Popular Question 4.9 years ago, created a question with more than 1,000 views. For How Does Average Heterozygosity Relate To Alellic Frequency Data

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