User: gabri.mochales

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Posts by gabri.mochales

<prev • 43 results • page 1 of 5 • next >
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Comment: 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.mochales30
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Comment: 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.mochales30
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Comment: C: Use fastQC and then multiQC on ddRAD fastq files ?
... 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.mochales30
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high sequence duplication ddRAD
... 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 ...
duplication ddrad snp sequencing written 22 days ago by gabri.mochales30 • updated 22 days ago by geek_y11k
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Tutorial STACKS ddRADseq
... 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 ...
stacks ddradseq written 4 weeks ago by gabri.mochales30
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Heterozygous individuals and FastaAlternateReferenceMarker
... 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 ...
fasta gatk snp written 9 weeks ago by gabri.mochales30
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Multisample VCF to FASTA
... 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 ...
vcf fasta gatk written 12 weeks ago by gabri.mochales30 • updated 12 weeks ago by Kevin Blighe63k
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SNP calling specific genes with GATK
... 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 ...
vcf gatk target capture target-capture sequencing written 3 months ago by gabri.mochales30 • updated 3 months ago by bruce.moran840
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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.mochales30
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quality check of bam files
... 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 ...
gatk quality bam sam written 3 months ago by gabri.mochales30 • updated 3 months ago by Pierre Lindenbaum129k

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