User: Fabio Marroni
Fabio Marroni • 2.6k
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Posts by Fabio Marroni
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... Try `samtools faidx ./file_1.fasta -i MHLFILTNLILPAFEDLAQG` or `samtools faidx -i ./file_1.fasta MHLFILTNLILPAFEDLAQG` ...
written 6 weeks ago by
Fabio Marroni • 2.6k
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Comment:
C: samtools subsampling reads
... The pattern is perfectly fine, and statistically expected. Highly covered regions in the original genome, are also more likely to be sampled by random sampling, so you will always (more or less) keep the same pattern of coverage, but at lower levels. ...
written 6 weeks ago by
Fabio Marroni • 2.6k
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Comment:
C: samtools subsampling reads
... Which samtools version are you using? Some time ago (I don't remember the version) you needed to use a comma delimited number in which the integer is the seed and the decimal the proportion you want to extract. I had similar issues, and posted everything here on Biostars. You can give a look at this ...
written 7 weeks ago by
Fabio Marroni • 2.6k
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... To get more help you should post the whole error message. However, it looks like either `de$cp1_LFC` or `de$cp1_padj` are not defined. ...
written 8 weeks ago by
Fabio Marroni • 2.6k
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... The files
seabass_index_dups.e8760153.1
seabass_index_dups.o8760153.1
seabass_index_dups.pe8760153.1
seabass_index_dups.po8760153.1
are the log files form your queuing system. Read them and see if there is an error. The missing files are probably due to the fact that the indexing ...
written 8 weeks ago by
Fabio Marroni • 2.6k
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165
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... Probably this isn't the problem, but the variance is (standard deviation)^2 while you are plotting sqrt(standard deviation). ...
written 10 weeks ago by
Fabio Marroni • 2.6k
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165
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... > "due to small sample size, p-values were not adjusted"
Wow! This is a sentence that I could write! However, my friends that know more about statistics would translate it as:
> "since we don't have enough power, in order to find some significant result, we will inflate type I error by not ...
written 11 weeks ago by
Fabio Marroni • 2.6k
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187
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... `head(phyloseq)` or `head(physeq)`? ...
written 3 months ago by
Fabio Marroni • 2.6k
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317
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Comment:
C: Why sortmerna 4.2.0 runs so slow?
... I would either try another installation (source code or conda), or ask authors for help. The behavior is strange indeed. ...
written 5 months ago by
Fabio Marroni • 2.6k
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317
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Comment:
C: Why sortmerna 4.2.0 runs so slow?
... Wow, I didn't even know about 4.2.0. I followed the link on the paper and got version 2.1. Just out of curiosity, are you using the binaries or you compiled from source code? I don't know if this could affect (it shouldn't but you never know). ...
written 5 months ago by
Fabio Marroni • 2.6k
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