Admin: Pierre Lindenbaum
Pierre Lindenbaum ♦ 125k
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- France/Nantes/Institut du Thorax - INSERM UMR1087
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- http://plindenbaum.blo...
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Posts by Pierre Lindenbaum
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... Using samjdk: http://lindenb.github.io/jvarkit/SamJdk.html
and the following snippet.
final boolean accept=true;
final String contig="RF02";
final byte base='A';
final int position=877;
if(record.getReadUnmappedFlag()) return accept;
if(!record.getContig().equals( ...
written 1 hour ago by
Pierre Lindenbaum ♦ 125k
0
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... please flag the question as answered if it fulfills your needs (green tick on the left) ...
written 1 hour ago by
Pierre Lindenbaum ♦ 125k
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33
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... see https://string-db.org/cgi/download.pl
in the **SQL** dump evidence_schema.v11.0.sql.gz (13.2 Gb) ...
written 4 hours ago by
Pierre Lindenbaum ♦ 125k
0
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... how was formatted you fasta sequence
can you verifiy that the chromosome is present in the *.fasta , *.fai and the *.dict files.
...
written 21 hours ago by
Pierre Lindenbaum ♦ 125k
0
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... using vcffilterjdk: http://lindenb.github.io/jvarkit/VcfFilterJdk.html
java -jar dist/vcffilterjdk.jar -rc -e 'return new VariantContextBuilder(variant).genotypes( variant.getGenotypes().stream().map(G->{ if(!G.hasAD() || !G.isHet()) return G; final int ad[]=G.getAD(); if(ad.length!=2) ret ...
written 22 hours ago by
Pierre Lindenbaum ♦ 125k
2
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1
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... using eutils
$ seq 2000 2020 | while read Y ; do wget -q -O - "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=cancer[TIAD]+${Y}[PDAT]&rettype=count" | xmllint --xpath '/eSearchResult/Count/text()' - && echo " $Y"; done
70841 2000
73077 2001
...
written 1 day ago by
Pierre Lindenbaum ♦ 125k
0
votes
1
answer
46
views
1
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... please mark the question as answered, (green mark on the left) ...
written 1 day ago by
Pierre Lindenbaum ♦ 125k
1
vote
1
answer
46
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1
answers
... try to change this line: https://github.com/JamesABaker/complexity_in_pymol/blob/46b044d13b7930455878aab42e1fbdfd3f05eea4/pymol/phobius.pl#L32 ...
written 1 day ago by
Pierre Lindenbaum ♦ 125k
0
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1
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46
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1
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... As far as I can see there is not such option "**color**" in gnuplot: http://gnuplot.sourceforge.net/docs_4.2/node409.html
set terminal png
{{no}transparent} {{no}interlace}
{{no}truecolor} {rounded|butt}
{tiny | small | medium | large | giant}
{ ...
written 1 day ago by
Pierre Lindenbaum ♦ 125k
0
votes
1
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48
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1
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... > or script that can use a sam file aligned to a consensus where I can modify the base at a specific location
see https://www.biostars.org/p/404363
...
written 1 day ago by
Pierre Lindenbaum ♦ 125k
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