Admin: Pierre Lindenbaum

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Posts by Pierre Lindenbaum

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Answer: A: miRanda target information extraction
... > But I only want this info from the ones with the hits (miRNA-target Sequence Alignment), like entry #1 grep -A 1 -m 1 > entry #2 grep -A 1 -m 2 | tail -1 ...
written 4 hours ago by Pierre Lindenbaum89k
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Comment: C: Failed in Fastqc, wiht out final report
... there's something wrong in the FASTQC installation: /etc/fastqc/Configuration/adapter_list.txt doesn't exist. Check the parameters of fastqc ...
written 9 hours ago by Pierre Lindenbaum89k
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Answer: A: gnu parallel for RNA seq
... try echo -e "WT1\nWT2\nVD1\nVD2" | parallel -- 'cufflinks -g gencode.v21.annotation.gtf -o {} /home/k/{}/accepted_hits.bam' ? ...
written 9 hours ago by Pierre Lindenbaum89k
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Answer: A: Modifying NCBI identifiers in BLAST output
... awk -F '\t' '{OFS="\t";split($2,a,/\|/);$2=a[4];print;}' input.tsv > output.tsv ...
written 21 hours ago by Pierre Lindenbaum89k
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Comment: C: How to get RID from blast rest api url using php
... so , you are able to retrieve the RID. What's you're problem ? ...
written 1 day ago by Pierre Lindenbaum89k
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Answer: A: How to get RID from blast rest api url using php
... > I don't know how to get that RID you have to "grep" the RID in the BLAST output: curl -sL "https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Put&QUERY=SSWWAHVEMGPPDPILGVTEAYKRDTNSKK&PROGRAM=blastp&FILTER=L&DATABASE=nr&FORMAT_TYPE=XML" | grep "RID = " RID = AGRY2BN ...
written 1 day ago by Pierre Lindenbaum89k
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Comment: C: Download custom track from UCSC genome browser to local
... what kind of track ? bed ? wig ? bam ?... ...
written 1 day ago by Pierre Lindenbaum89k
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Answer: A: SnpSift command query
... try '||' (OR operator) instead of '|' (bitwise inclusive OR operator) ...
written 2 days ago by Pierre Lindenbaum89k
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Answer: A: Shuffle Reads Prior to Alignment With BWA-mem
... linearize, add a random number, sort on this random number, remove this first column convert back to fastq, compress gunzip -c input.fastq.gz | paste - - - - - - - - | awk -F '\t' '{printf("%f\t%s\n",rand(),$0);}' | LC_ALL=C sort -t $'\t' -k1,1g | cut -f 2- | tr "\t" "\n" | gzip > suffl ...
written 2 days ago by Pierre Lindenbaum89k
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Comment: C: Shuffle Reads Prior to Alignment With BWA-mem
... > GATK tutorial that the reads in these files should be sorted randomly it's true if the fastq have been generated from a previously-ordered bam: the order of the reads is non-random and so there is a bias in the estimation of the average fragment length. ...
written 2 days ago by Pierre Lindenbaum89k

Latest awards to Pierre Lindenbaum

Appreciated 5 hours ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Teacher 7 hours ago, created an answer with at least 3 up-votes. For A: How To Get Gene Regions +3Kb Upstream
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: How To Get Gene Regions +3Kb Upstream
Scholar 3 days ago, created an answer that has been accepted. For A: How to cut fasta sequences in three equivalement parts ?
Scholar 3 days ago, created an answer that has been accepted. For A: How to cut fasta sequences in three equivalement parts ?
Appreciated 3 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: How To Get Gene Regions +3Kb Upstream
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: How To Get Gene Regions +3Kb Upstream
Scholar 3 days ago, created an answer that has been accepted. For A: How to cut fasta sequences in three equivalement parts ?
Teacher 4 days ago, created an answer with at least 3 up-votes. For A: How To Get Gene Regions +3Kb Upstream
Good Answer 5 days ago, created an answer that was upvoted at least 5 times. For A: How To Get Gene Regions +3Kb Upstream
Good Answer 5 days ago, created an answer that was upvoted at least 5 times. For A: How Can I Get The Human Chromosome Centromere Position And Chromosome Length In
Appreciated 6 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: How To Get Gene Regions +3Kb Upstream
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: How To Get Gene Regions +3Kb Upstream
Good Answer 12 days ago, created an answer that was upvoted at least 5 times. For A: How To Get Gene Regions +3Kb Upstream
Appreciated 16 days ago, created a post with more than 5 votes. For GNU datamash ( command-line program which performs simple calculation)
Appreciated 17 days ago, created a post with more than 5 votes. For GNU datamash ( command-line program which performs simple calculation)
Scholar 17 days ago, created an answer that has been accepted. For A: How to cut fasta sequences in three equivalement parts ?
Teacher 17 days ago, created an answer with at least 3 up-votes. For A: How To Get Gene Regions +3Kb Upstream
Scholar 18 days ago, created an answer that has been accepted. For A: How to cut fasta sequences in three equivalement parts ?
Scholar 18 days ago, created an answer that has been accepted. For A: How to cut fasta sequences in three equivalement parts ?
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: How To Get Gene Regions +3Kb Upstream
Appreciated 20 days ago, created a post with more than 5 votes. For GNU datamash ( command-line program which performs simple calculation)

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