Admin: Pierre Lindenbaum

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France/Nantes/Institut du Thorax - INSERM UMR1087
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Posts by Pierre Lindenbaum

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Answer: A: bamtools filter specific motif sequence
... samtools view -h input.bam | awk -F '\t' '($1 ~ /^@/ || $10 ~/AAACCTG/ )' | samtools view -Sb -o out.bam using [samjs][1] java -jar dist/samjs.jar -e 'record.getReadString().contains("AAACCTG")' input.bam [1]: https://github.com/lindenb/jvarkit/wiki/SamJS ...
written 3 hours ago by Pierre Lindenbaum91k
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Answer: A: Depleting BED file of specific regions
... bedtools intersect http://bedtools.readthedocs.io/en/latest/content/tools/intersect.html ...
written 10 hours ago by Pierre Lindenbaum91k
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Comment: C: Question: Mean and SD read length from a range of fastq files
... please mark this question as answered (green tick on the left) ...
written 10 hours ago by Pierre Lindenbaum91k
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Comment: C: Question: Mean and SD read length from a range of fastq files
... for F in *.fasq do echo "$F " awk '(... same... script)' $F done ...
written 11 hours ago by Pierre Lindenbaum91k
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Comment: C: Picard Build Failure
... Hello NGS-Newbie! It appears that your post has been cross-posted to another site: https://github.com/broadinstitute/picard/issues/777 This is typically not recommended as it runs the risk of annoying people in both communities. ...
written 1 day ago by Pierre Lindenbaum91k
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Answer: A: Question: Mean and SD read length from a range of fastq files
... Using awk: awk 'BEGIN { t=0.0;sq=0.0; n=0;} ;NR%4==2 {n++;L=length($0);t+=L;sq+=L*L;}END{m=t/n;printf("total %d avg=%f stddev=%f\n",n,m,sq/n-m*m);}' *.fastq ...
written 1 day ago by Pierre Lindenbaum91k
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Comment: C: Publication ethics and authorship guidelines
... you could also ask: https://academia.stackexchange.com/ * https://academia.stackexchange.com/search?q=publishing+advisor * Publishing my work without advisor https://academia.stackexchange.com/questions/31266/publishing-my-work-without-advisor ...
written 1 day ago by Pierre Lindenbaum91k
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Comment: C: VCF Files: Help on 0/1 1/1 0/0 1/1 | vs / (phased & unphased
... homref -> 0/0 homvar -> 1/1 het -> 0/1 ...
written 1 day ago by Pierre Lindenbaum91k
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Answer: A: Sorting .bam file by tag
... Using awk and the tag 'NM' (insert a column containing the sort key, void for headers) samtools view -h input.bam |\ awk -F '\t' 'NR==1 {printf("\t@HD\t%s\tSO:unsorted\n",$2);next} /^@/ {printf("\t%s\n",$0);next;} {v="";for(i=12;i<=NR;++i) {split($i,a,/[\:]/);if(a[1]=="NM") {v=a[3];bre ...
written 1 day ago by Pierre Lindenbaum91k
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Answer: A: NCBI esearch on multiple database
... **Performing a Global Entrez Search** : https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Performing_a_Global_Entrez_Sear ...
written 1 day ago by Pierre Lindenbaum91k

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Scholar 10 hours ago, created an answer that has been accepted. For A: How to cut fasta sequences in three equivalement parts ?
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Scholar 4 days ago, created an answer that has been accepted. For A: How to cut fasta sequences in three equivalement parts ?
Popular Question 5 days ago, created a question with more than 1,000 views. For samtools 1.0 'index' : CSI index vs BAI index ?
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Scholar 10 days ago, created an answer that has been accepted. For A: How to cut fasta sequences in three equivalement parts ?
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Scholar 11 days ago, created an answer that has been accepted. For A: How to cut fasta sequences in three equivalement parts ?
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Teacher 11 days ago, created an answer with at least 3 up-votes. For A: How To Get Gene Regions +3Kb Upstream
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