User: stuart archer

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Posts by stuart archer

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Does trimming RNA-Seq reads affect the differentially expressed genes?
... My trimviz tool can trace the 'fate' of trimmed reads in your alignments, if that helps: https://github.com/MonashBioinformaticsPlatform/trimviz You can see the alignment fate of trimmed reads in trimviz FQ, by adding in the bam file and reference genome (in addition to the pre-trimmed and post-tr ...
written 4 weeks ago by stuart archer70
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Tool: Trimviz, a lightweight QC tool to assess impact of read-trimming and aligner soft-clipping
... Hi all, I've found that with a lot of read-trimming tools (and also soft-clipping aligners), it's a little hard to assess whether trimming / filtering / clipping is justified. How do you know they are doing what you think they are doing? It's hard to tell by just digging through the resulting fastq ...
trimming tool fastq clipping alignment qc written 4 weeks ago by stuart archer70
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Comment: C: Keeping paired reads together when sorting BAM file by name
... Actually I just realised there is a utility in Rsubread ("repair") that is meant to take a location-sorted bam file as input and place the read-pairs together. See http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf ...
written 8 months ago by stuart archer70
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Comment: C: Creating a Contingency Table (Gene Absence Presence)
... Not sure about exactly how you'd build a contigency table here for chi2 or fishers. How about permuting the data and seeing whether the observed distance values fall outside the distribution for distance values from a 1000 random permutations y=matrix(c(sample(c(T,F), 100, T)), nrow=5, ncol = 2 ...
written 9 months ago by stuart archer70
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Comment: C: Creating a Contingency Table (Gene Absence Presence)
... OK I think I understand a bit better. You have two different questions: 1) Making trees out of pre-calculated distances between your clusters that you generated with BiG-SCAPE, which have nothing to do with the presence/absence data. For this I made what I think is a similar long-format table of pr ...
written 9 months ago by stuart archer70
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Comment: C: Creating a Contingency Table (Gene Absence Presence)
... Hi, so: > would my level of intensity in the heatmap be regulated by how absent > or present a given cluster is in a genome This is just 0 or 1, present or absent as far as I understand your data. You can construct trees, but they are not indicative of evolutionary relationships. To do this ...
written 9 months ago by stuart archer70
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Answer: A: Creating a Contingency Table (Gene Absence Presence)
... There are a few options, you can convert to a 1/0 matrix using table and 'image' the matrix. The gplots library has a convenient heatmap.2 function that will also cluster the rows and columns. I took some liberties with your data to include S.hygroscopicus twice so that clustering makes sense. ...
written 9 months ago by stuart archer70
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Comment: C: Trimming fastq up until a sequence
... To verify your trimming results, you might like to clone our visualisation tool [Trimviz][1], see example report [here][2] (currently in beta testing). I apologize for the shameless plug, but it's exactly this kind of non-standard trimming situation for which I envisaged it would be useful. Dependen ...
written 9 months ago by stuart archer70
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Comment: C: Trimming the metagenomics data
... In your Trimmomatic command, not sure why you escaped the colons in the ILLUMINACLIP bit (\:2\:30\:10) but not the other colons? Also, Trimmomatic is very fussy about the format of the sequence names in the .fa file so it would help to add the relevant part of that file to your question. By 'metagen ...
written 10 months ago by stuart archer70
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Answer: A: Keeping paired reads together when sorting BAM file by name
... I guess this is an old issue but I also ran into this problem with `samtools sort -n` ; I would just like it to sort by read name, but then preserve the original order from the aligner which places the read pairs together and makes it easier to parse. There is already an issue on samtools github re ...
written 13 months ago by stuart archer70

Latest awards to stuart archer

Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Creating a Contingency Table (Gene Absence Presence)
Scholar 9 months ago, created an answer that has been accepted. For A: Creating a Contingency Table (Gene Absence Presence)

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