User: Bastien Hervé
Bastien Hervé • 1.3k
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Posts by Bastien Hervé
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... I think I got something :
I downloaded your genbank file and I look at position 28770 of the sequence, the sequence is actually `gccgtcgg` not `CGGCAGCC` like in your `example_lines` variable.
Instead of `print(seq)` write `print(genome.seq[pos:pos+len(seq)])` and you will see the problem
The min ...
written 3 days ago by
Bastien Hervé • 1.3k
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... Try to investigate but you just have the reverse not the complement.
The reverse of `CGGCAGCC` is actually `CCGACGGC` ...
written 3 days ago by
Bastien Hervé • 1.3k
2
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... You want to remove unaligned reads ?
samtools view -F 4 ...
written 3 days ago by
Bastien Hervé • 1.3k
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... It's always clearer with an example. Do you want to access the sequence of your read using `chr1:100-120` or the possible gene at this position ?
Could you detailed this please :
>I want to know the location ...
written 4 days ago by
Bastien Hervé • 1.3k
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150
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... From this [thread][1], try under R :
counts <- read.table(file="/path/to/counts.csv", sep="\t", header=TRUE, row.names=1)
samples <- read.table(file="/path/to/samples.csv", sep="\t", header=TRUE)
counts$id <- row.names(counts)
mdfa <- reshape2::melt(counts, id.vars = "id ...
written 11 days ago by
Bastien Hervé • 1.3k
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Comment:
C: Mapping columns based on a list
... What are you thinking when you say :
> How I can map barcodes to sample numbers?
Could you make a example of the expected results please
Are you using R, Python, Perl... ?
Your raw counts are in files, dataframe or matrix ? ...
written 11 days ago by
Bastien Hervé • 1.3k
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... Opened discussion : If OP want to call variants, is it not a bit dangerous to use only "primary assembly" ?
Let's say that chr6_FIXED is a fixed part of chr6 that will be added in the next major release. This modification change a A to a T. In primary assembly you don't have this chr6_FIXED but you ...
written 11 days ago by
Bastien Hervé • 1.3k
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2
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178
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... Thank a lot for this very helpful comment. It took me around a hour to fully get the content with drawing and all.
Biologicaly I did not know that proteins could have so many binding sites. In my mind, proteins could have linked to a dozen binding sites not 10,000.
Do you have complementary inform ...
written 12 days ago by
Bastien Hervé • 1.3k
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... How do you distinguish PCR duplicates from "biological" duplicates ? You could loose 96% of your reads, that's a really hard filter. I mean in a whole genome analysis, then, OK you can filter out duplicates because you have a very low probability to sequence twice the same read, but in amplicon or c ...
written 12 days ago by
Bastien Hervé • 1.3k
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107
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... maybe this would work :
bedtools getfasta -fi genome.fa -bed <(echo awk -v OFS="\t" '{print $1,$2,$2+2,$4"\n"$1,$3-1,$3+1,$4}' input.bed) ...
written 12 days ago by
Bastien Hervé • 1.3k
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