User: dariober

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dariober8.6k
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Posts by dariober

<prev • 749 results • page 1 of 75 • next >
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Answer: A: How to get the coordinations of CpG sites in non-human genome
... This program I wrote [fastaRegexFinder][1] could help you. You could get the positions of CpGs in bed format with something like: fastaRegexFinder.py -f genome.fa -r CG --noreverse > CpG.bed But yes, finding CpG is quite easy in case you want to give it go writing your own script. [1]: h ...
written 3 days ago by dariober8.6k
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Comment: C: TMB Tumor Mutation Burden
... I think the "number of mutations per magabase" could be a misleading estimate of TMB. The deeper you sequence the more mutations per magabase you find since you detect more and more variants with low allele frequency. Maybe one should weight a variant by its frequency in order to compute TMB. (NB, I ...
written 3 days ago by dariober8.6k
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Comment: C: Sorting file by column, with missing values
... Are you sure the file is tab-separated? You can check with `cat -vet file.txt` and see if columns are separated by the `^I` marker. Also, you probably want `-k8,8nr` to sort column 8 numerically largest to smallest rather than alphanumerically. ...
written 7 days ago by dariober8.6k
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Answer: A: Plotting common SNPs from four individual from a vcf file
... Once again, I'm going to suggest [UpSetR][1]. A venn diagram with four intersections starts being quite messy. [1]: https://github.com/hms-dbmi/UpSetR ...
written 7 days ago by dariober8.6k
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Answer: A: MuTect2 still discard many reads, how to fix?
... If you are sure you want to retain non primary and duplicates, I think you can add to mutect the option `--disable_read_filter NotPrimaryAlignmentFilter --disable_read_filter DuplicateReadFilter` (not tested). See some docs [here.][1] [1]: https://software.broadinstitute.org/gatk/documentation/t ...
written 7 days ago by dariober8.6k
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Answer: A: Ideas to plot several enrichment results (BP) in one
... Maybe something along the lines of [UpSetR][1] would work? [1]: https://github.com/hms-dbmi/UpSetR ...
written 8 days ago by dariober8.6k
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Comment: C: WGS data for pipeline development
... Not really answering your question but maybe useful tips... To add Read Group to your bam files, run `bwa mem` with the `-R STR` options. This way you can eliminate the AddOrReplaceReadGroup step. Also, consider piping the output of `bwa mem` to `samtools sort` so you get the sorted bam file without ...
written 11 days ago by dariober8.6k
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Comment: C: Importing Uniprot into BioSQL using BioPython takes years (nearly literally!)
... Sorry, I can't be more specific as I'm not familiar with BioSQL and, of course, with your task. But... > in principle I only need the sequence and the organism... I wanted to say this in my first comment... Maybe you should move away from BioSQL altogether and parse the xml files to extract wha ...
written 12 days ago by dariober8.6k
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Comment: C: Importing Uniprot into BioSQL using BioPython takes years (nearly literally!)
... This may be a long shot... Try to move the `server.commit()` outside the while loop. *I.e.* load everything first and then commit in bulk. By the way, it seems that most of the code of [BioSql][1] is 8-10 years old. Maybe it is not tuned to cope with the amount of data you have. [1]: https://git ...
written 12 days ago by dariober8.6k
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Answer: A: CosmicCodingMuts.vcf.gz for hg38?
... This is the script I used to prepare the cosmic file for mutect2 (GATK 3.8). Check if it suites you (and does the right thing!). I think I had to get a user account for [Cosmic][1] first: ## Edit to put your email address: sftp @@sftp-cancer.sanger.ac.uk sftp> get /files/grch38 ...
written 16 days ago by dariober8.6k

Latest awards to dariober

Scholar 7 days ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Good Answer 8 days ago, created an answer that was upvoted at least 5 times. For A: count the number of transcription factor binding sites
Appreciated 10 days ago, created a post with more than 5 votes. For A: Output the color code according to number
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Trim & align paired-end reads in a single pass
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: Output the color code according to number
Good Answer 11 weeks ago, created an answer that was upvoted at least 5 times. For A: count the number of transcription factor binding sites
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Scholar 3 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Scholar 3 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Filtration Of Reads With Length Lower Than 30 From Bam
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: What is the reason for trimming reads to 30 bp for ATAC-seq aligning?
Popular Question 4 months ago, created a question with more than 1,000 views. For Trim & align paired-end reads in a single pass
Great Question 5 months ago, created a question with more than 5,000 views. For Add read group to header after samtools merge
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Filtration Of Reads With Length Lower Than 30 From Bam
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Student 6 months ago, asked a question with at least 3 up-votes. For ChIP-Seq: Calling peaks with replicates
Appreciated 7 months ago, created a post with more than 5 votes. For A: Output the color code according to number
Scholar 7 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: count the number of transcription factor binding sites
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Filtration Of Reads With Length Lower Than 30 From Bam
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets

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