User: toni

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toni2.2k
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Bioinformatician. Interested in genomics, trancriptomics, NGS.

Posts by toni

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Answer: A: Calculate percentage of bases covered less than nX in targeted sequencing experi
... I know it's an old thread but as I have tested this tool recently, I would definitely use [Mosdepth][1] to answer this question. It's fast and its `--thresholds` option does exactly this. Anthony [1]: https://github.com/brentp/mosdepth ...
written 2.2 years ago by toni2.2k
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Comment: C: Final Solution For "Mapq Should Be 0 For Unmapped Read."
... If you read carefully, this is already said in the first line of the question itself. ...
written 4.5 years ago by toni2.2k
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Comment: C: how to calculate the correlation and p values for all combination of a gene expr
... Looks like there are too many questions in one : 1 - What should I use to test my geneXgene correlations ? 2 - How to adjust my p-values to get the significant ones (Multiple Hypothesis Testing) or how to rank (arbitrary threshold) ?  3 - What is the general approach for that kind of problem ? 4 ...
written 5.7 years ago by toni2.2k
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Answer: A: Does build 37 of the human reference genome contain 2.85Gbp?
... I have computed this recently on GRCh37 :     (Mappability was computed with GEM program for reads of length 100 and 5 mismatches authorised) EDIT : And so dividing by 2.85Gb gives you a more realistic estimate of your mean coverage since N's will never be covered by definition.   ...
written 5.7 years ago by toni2.2k
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Comment: C: Multiline Fasta To Single Line Fasta
... I do not think that this is a good advice for several reasons (even if it can work in a few cases): - FASTA files are sometimes BIG, like 20Gb, containing millions of records. Not sure whether Notepad will survive to this. - (I think) This forum/site is more about learning/developing some coding s ...
written 5.9 years ago by toni2.2k
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Answer: C: Does read-depth refer to a fold?
... No. You should rather see this as a multiplicative factor. Increased by 3-fold means : NEW = 3 * OLD     ...
written 6.0 years ago by toni2.2k
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Comment: C: Markduplicates Creating A Loss Of Mate Pair
... This is the behavior I always had with MarkDuplicates when removing them. It generates orphan reads. These orphan reads are unmapped. Actually, it happens when you have a pair where only one read is mapped. When this mapped read is tagged as a duplicate, MarkDuplicate leaves its unmapped mate in t ...
written 7.0 years ago by toni2.2k
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Answer: A: Split Fastq Paired-Read Using Awk
... If you are sure that pair F3 is ALWAYS written before pair G3, you can try this : awk 'BEGIN{count=0}{count++; if(count<=4) {print $0 > "F3.fastq"} else {print $0 > "R3.fastq" } if(count==8) count=0 }' input.fastq ...
written 7.5 years ago by toni2.2k
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Comment: C: How To Extract Consensus Sequence Of Mapped Regions From A Bam File?
... You might find this thread or this link useful for your purpose. How to generate a consensus fasta sequence from SAM tools pileup? http://chipster.csc.fi/manual/samtools-consensus.html ...
written 7.6 years ago by toni2.2k
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Comment: C: Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
... I do agree. How many times (I am not going to cite the tools) in my team we have been lost into tool "bugs". We have spent a incredible amount of time running a tool to see it crash in the end, and for some tools it could fail after one week. You also sometimes report this to the developer and you s ...
written 7.6 years ago by toni2.2k

Latest awards to toni

Appreciated 5 months ago, created a post with more than 5 votes. For A: Replacing Dots In File
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Replacing Dots In File
Epic Question 10 months ago, created a question with more than 10,000 views. For Gff3 Format - Human Genome
Epic Question 15 months ago, created a question with more than 10,000 views. For Ngs - Huge (Fastq) File Parsing - Which Language For Good Efficiency ?
Popular Question 19 months ago, created a question with more than 1,000 views. For C: How To Extract Consensus Sequence Of Mapped Regions From A Bam File?
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: How To Parse Fastq File?
Great Question 4.4 years ago, created a question with more than 5,000 views. For Library Duplicates Vs. Optical Duplicates (Picard Markduplicates)
Great Question 4.8 years ago, created a question with more than 5,000 views. For Gff3 Format - Human Genome
Great Question 5.2 years ago, created a question with more than 5,000 views. For Gff3 Format - Human Genome
Popular Question 5.2 years ago, created a question with more than 1,000 views. For Gff3 Format - Human Genome
Teacher 5.4 years ago, created an answer with at least 3 up-votes. For A: How To Parse Fastq File?
Scholar 5.4 years ago, created an answer that has been accepted. For A: Does build 37 of the human reference genome contain 2.85Gbp?
Epic Question 5.4 years ago, created a question with more than 10,000 views. For Ngs - Huge (Fastq) File Parsing - Which Language For Good Efficiency ?
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: How To Parse Fastq File?
Good Question 5.6 years ago, asked a question that was upvoted at least 5 times. For Gff3 Format - Human Genome
Scholar 5.7 years ago, created an answer that has been accepted. For A: Does build 37 of the human reference genome contain 2.85Gbp?
Good Answer 5.7 years ago, created an answer that was upvoted at least 5 times. For A: Sam Validation Error: Error: Record 8404072, Read Name Srx020270.6546275, Mapq S
Teacher 5.8 years ago, created an answer with at least 3 up-votes. For A: How To Parse Fastq File?
Commentator 5.9 years ago, created a comment with at least 3 up-votes. For C: Useful Bash Commands To Handle Fasta Files
Popular Question 6.1 years ago, created a question with more than 1,000 views. For Selecting Nodes Of High Correlation In A Tree

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