Moderator: h.mon

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h.mon31k
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Posts by h.mon

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Comment: C: freebayes error variant calling
... **SM** is sample, not read group. ...
written 26 days ago by h.mon31k
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Comment: C: Where to find annotation infos for my Expressionset?
... How did you create the expressionSet object? Did you create an annotation creating the object? Please post you code and more information about your expressionSet so we have the necessary information to help you. ...
written 27 days ago by h.mon31k
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Answer: A: Metagenomic Data management
... **edit:** name of the script changed from **weird_to_long.pl** to **weird_to_wide.pl**. I hacked a small Perl script to convert the data. Save the script as `weird_to_wide.pl` and run as (you may need to `chmod +x weird_to_wide.pl`): ./weird_to_wide.pl < input.tsv > output.tsv In the pr ...
written 28 days ago by h.mon31k
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Comment: C: BWA aligning forward and reverse differently
... I see what you mean, and I don't have an answer as to why bwa behaves like it does. My only suggestion would be to try a global aligner, e.g., BBMap or Bowtie2 with the `--end-to-end` flag. I have blasted the read, and it maps to 2 different chromosomes in a RefSeq genome - the 72 initial bases mat ...
written 28 days ago by h.mon31k
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Comment: C: how to get one vcf file for freebayes from many bam files
... And if you didn't add read groups when mapping, there is a small utility ([bamaddrg][1]) by the same main FreeBayes author which allows adding read groups to several bam files and streaming the output into freebayes. [1]: https://github.com/ekg/bamaddrg ...
written 29 days ago by h.mon31k
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Answer: A: Ensembl reference genomes and annotations by chromosome only.
... I have downloaded several genomes and annotations from Ensembl, each contained in single genome (fasta) and annotation (gff or gtf) files. It may be a bit confusing at first, with all the **.dna.chromosome.1.fa.gz** and **.chromosome.X.gff3.gz**, but you just want the files with no **chromosome** i ...
written 29 days ago by h.mon31k
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Comment: C: Blastn raw illumina reads all-against-all and return only non-hits
... Did you consider alternative approaches? For example, performing kmer set operations will probably be a lot faster than blasting and parsing the output. A search for **kmer set operations** will return a good amount of alternatives. I have used [KmerCrompressor][1] a couple of times and it was fas ...
written 29 days ago by h.mon31k
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Answer: A: BWA aligning forward and reverse differently
... These two reads are a pair, and they aren't identical - although they fully overlap, and one is the reverse-complement of the other. My guess is even with such high penalty, for the second read in the pair soft-clipping must have been cheaper than extending the mapping. How can I be so certain thes ...
written 29 days ago by h.mon31k
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Comment: C: Using Trinity for DGE - how to input study design
... Trinity provides wrapper scripts to automate DGE analysis, see [Differential Expression Analysis Using a Trinity Assembly][1]. The wrapper scripts will create the R code on the fly, you can then open this code and modify the DGE analysis scripts to suit your needs. [1]: https://github.com/trinit ...
written 29 days ago by h.mon31k
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Comment: C: Number of replicates in each group in RNA seq
... It probably depends on which tool you will use for analysis, but for several tools it doesn't matter. See an answer (and several links) here: https://www.biostars.org/p/369328/ ...
written 29 days ago by h.mon31k

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