Moderator: Bastien Hervé
Bastien Hervé ♦ 4.3k
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Posts by Bastien Hervé
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... Prokka would have help if you were looking at gene location on your genomes ...
written 14 days ago by
Bastien Hervé ♦ 4.3k
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... If I got you right you are trying to get unique parts of your 3 genomes to create a single one without redundancy. I do not think you can do that in a linear standard way.
If you want to analyze your genes of your 28 genomes based on your 3 other genomes you can try [Prokka][1]
If you want to alig ...
written 15 days ago by
Bastien Hervé ♦ 4.3k
• updated
15 days ago by
ATpoint ♦ 18k
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Comment:
C: RNA Seq, annotation, RNA Class
... You can have a look at [BiomaRt][1] from Ensembl
[1]: https://bioconductor.org/packages/release/bioc/html/biomaRt.html ...
written 26 days ago by
Bastien Hervé ♦ 4.3k
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... Why not using samtools ? You can take a look at `man sort`
https://unix.stackexchange.com/questions/52762/trying-to-sort-on-two-fields-second-then-first ...
written 4 weeks ago by
Bastien Hervé ♦ 4.3k
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... Hello https://www.biostars.org/u/55198/
Is it what you are looking for ? If you have solo line fasta this should work otherwise a python solution may be more suitable
cat reads.fa | sed 's/>/@/g' | paste - - <(seq -w 1 $(grep -c ">" reads.fa) | xargs printf '+\n%.s') <(awk 'NR % 4 ...
written 4 weeks ago by
Bastien Hervé ♦ 4.3k
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... I would be interested to know if there are some criticals bias too !
A start in this Intro : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5976456/ ...
written 5 weeks ago by
Bastien Hervé ♦ 4.3k
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... 1) No the phred33 option is use by default and will not filter out any reads based on their quality. It is a table cotation for score, on old sequencing machine phred64 table where used to report scores. Nowadays, sequencing machine use phred33 score table. I suggest you to not use this option at al ...
written 5 weeks ago by
Bastien Hervé ♦ 4.3k
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... You can try this one : https://bioconductor.org/packages/release/bioc/vignettes/ReactomePA/inst/doc/ReactomePA.html ...
written 5 weeks ago by
Bastien Hervé ♦ 4.3k
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... You can use TPM to compare gene count in the same sample, but it is not the best way to go to compare genes across sample, prefer RLE or TMM method for example.
This is one way to convert to TPM : https://support.bioconductor.org/p/91218/
Your function seems ok
See also : https://youtu.be/TTUrtCY ...
written 6 weeks ago by
Bastien Hervé ♦ 4.3k
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... > The "-q" parameter only filter out reads with MAPQ less then a specific value...therefore it is not working for me.
What do you mean ? Option `-q` will extract reads with mapping quality above or equal the threshold. You cannot recover your 0 mapping quality this way.
Even if you are able to ...
written 6 weeks ago by
Bastien Hervé ♦ 4.3k
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