User: gabri.mochales
gabri.mochales • 30
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Posts by gabri.mochales
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C: high sequence duplication ddRAD
... thanks to both of you, obviously I don't understand it as I thought. I'll check the papers! ...
written 22 days ago by
gabri.mochales • 30
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C: high sequence duplication ddRAD
... Thanks for answering. I'm aware of how ddRAD works, but what I don't understand is the pattern I observe in my data. I uploaded a picture, let's see if you can check it. ...
written 22 days ago by
gabri.mochales • 30
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... Heys, I'm in the same situation, I do get quite a lot of duplicates, did you solve it? ...
written 22 days ago by
gabri.mochales • 30
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... Hello,
I'm relatively new to NGS analyses. I'm working with single-read ddRAD data of a non-model species and we just obtained the fastq files. The company removed the adaptors and I've just did the demultiplexing and some trimming, to remove the overhangs. When I run FASTQC and MultiQC, I obtain a ...
written 22 days ago by
gabri.mochales • 30
• updated
22 days ago by
geek_y ♦ 11k
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... Heys,
I'm new to NGS analyses and I am really interested in ddRADseq analyses, specially with the software STACKS. Currently, I still do not have any data to analyze, so I was looking for a tutorial that provides some data to start training the analyses with the software STACKS. Do you have any reco ...
written 4 weeks ago by
gabri.mochales • 30
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... Good afternoon,
I am having a doubt with the function `FastaAlternateReferenceMarker` from GATK. I already have a phased VCF file and when I want to obtain the fasta files for some specific genes (giving the target genes sequences and the VCF file to the function) I just obtain one of the sequences ...
written 9 weeks ago by
gabri.mochales • 30
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... Good afternoon,
I know there are already quite a lot of posts explaining how to convert a VCF file to Fasta (In fact, I was using FastaAlternateReferenceMarker) but I did not find any solution for what I want to do. I have a multisampled and phased VCF file and I want to convert each one of the sam ...
written 12 weeks ago by
gabri.mochales • 30
• updated
12 weeks ago by
Kevin Blighe ♦ 63k
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... Good afternoon,
I'm trying to do the SNP calling of some files from a target-capture sequencing experiment with GATK. I don't have any problem but I've seen that with Freebayes I can do the SNP calling specifically of my target genes, and this would help me a lot to get the fasta files
freebaye ...
written 3 months ago by
gabri.mochales • 30
• updated
3 months ago by
bruce.moran • 840
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Comment:
C: quality check of bam files
... Like in [here][1] ? I don't fully get GATK BEst Practices
[1]: https://gatk.broadinstitute.org/hc/en-us/articles/360035535912 ...
written 3 months ago by
gabri.mochales • 30
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... Good afternoon,
I'm working with GATK to do the SNP calling of some target capture sequencing data. Right now I'm creating the bam files and I was wondering which are the standard quality measures I should apply to my bam files. I'm aware that I can mark duplicates, but I don't know how this could a ...
written 3 months ago by
gabri.mochales • 30
• updated
3 months ago by
Pierre Lindenbaum ♦ 129k
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