User: miles.thorburn

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Posts by miles.thorburn

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Comment: C: Keeping only matching reads in fastq files
... Exactly, and it is as simple as taking the columns of header names and only keep those entries. I haven't done that just yet, but I'll write the script soon. ...
written 4 days ago by miles.thorburn80
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Comment: C: Keeping only matching reads in fastq files
... I'll have a look. Thanks. I may have found a solution using `uclust` though. If you use the second fasta as the database, it will match all reads. ...
written 4 days ago by miles.thorburn80
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Comment: C: Keeping only matching reads in fastq files
... Yes, because we used 2 separate extractions for each individual that were sequenced in different lanes, we are trying to be careful to not incorporate erroneous alleles into our data set. Our estimations are that the genes are nearly as polymorphic as the MHC region, hence being so careful. ...
written 4 days ago by miles.thorburn80
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Keeping only matching reads in fastq files
... I have sequences from 2 separate extractions for the same individual. We are working on a highly polymorphic region, and only want to keep reads that are found in both fastq files (from separate Illumina lanes). I've already paired the sequences if that changes anything. The ideal tool would match ...
fastq written 5 days ago by miles.thorburn80 • updated 5 days ago by genomax68k
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Comment: C: Multiple Sequence Alignment for very large data sets
... Hi, the analysis changed quite significantly since then. I ended up using only needing to align coding sequences from my individuals and an outgroup. I did that was GUIDANCE and the MAFFT algorithm for codon alignments. Since the majority of my sequences came from the same individual, once I had t ...
written 5 weeks ago by miles.thorburn80
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Command Line HKA Test Software
... I am looking for a command line program that can perform the HKA test on fasta files. I have seen that programs like dnaSP are available, but I don't believe they are command line. Maybe I've missed a few, but I can't seem to find anything to calculate these values on a computing cluster. I would ...
hka written 6 weeks ago by miles.thorburn80
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Appropriate k-mer size for mappability mask
... As part of [MSMC][1], you need a mappability mask. However, for non-model organisms, you'll likely have to generate the masks yourself. I am using 3 spined sticklebacks, and my sequencing for each individual is comprised of 3 different libraries; 100bp reads with 140bp and 300bp insert sizes, and 50 ...
snpable mappability written 6 weeks ago by miles.thorburn80
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Answer: A: Visualisation of GO Terms
... In the end, I ended up getting the GO profile using a Bioconductor package [GOprofiles][1]. I converted the Ensembl stable gene IDs to Entrez IDs using Ensembl's Biomart tool. There is a small amount of information loss here - as with almost every step here - as some of the Ensembl genes did not hav ...
written 7 weeks ago by miles.thorburn80
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Comment: C: Visualisation of GO Terms
... Thanks, I have seen the GOBPCHILDREN and ancestor tool in that package. But as you said, it's not a 1:1 relationship so I fear I would not get the values correct for each of the parent terms. ...
written 7 weeks ago by miles.thorburn80
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Comment: C: Visualisation of GO Terms
... Thanks. I'll have a look at the tool. ...
written 7 weeks ago by miles.thorburn80

Latest awards to miles.thorburn

Scholar 3 months ago, created an answer that has been accepted. For A: Filtering VCFs and Phasing
Scholar 3 months ago, created an answer that has been accepted. For A: Filtering VCFs and Phasing
Scholar 5 months ago, created an answer that has been accepted. For A: Filtering VCFs and Phasing
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