User: Bastien Hervé

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Bastien Hervé1.3k
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Location:
Limoges, CBRS, France
Last seen:
7 hours ago
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1 year, 4 months ago
Email:
b****************@orange.fr

Posts by Bastien Hervé

<prev • 276 results • page 1 of 28 • next >
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Answer: A: Trouble locating a known motif on (-) strand: any hints for a beginner?
... 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 Hervé1.3k
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Comment: C: Trouble locating a known motif on (-) strand: any hints for a beginner?
... 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 Hervé1.3k
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Answer: C: How extract aligned exactly 1 time in Single end read?
... You want to remove unaligned reads ? samtools view -F 4 ...
written 3 days ago by Bastien Hervé1.3k
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Comment: C: pysam: Use read ID to access location
... 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 Hervé1.3k
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Answer: A: Mapping columns based on a list
... 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 Hervé1.3k
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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 Hervé1.3k
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Comment: C: Fasta file and GTF file for STAR alignment
... 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 Hervé1.3k
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Comment: C: Did you remove ChIP-seq duplicates
... 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 Hervé1.3k
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Comment: C: Did you remove ChIP-seq duplicates
... 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 Hervé1.3k
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Comment: C: nucleotide extraction using coordinates
... 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 Hervé1.3k

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