User: dariober

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dariober8.0k
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Posts by dariober

<prev • 690 results • page 1 of 69 • next >
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Comment: C: VIew reads sorted by name in IGV
... Hi- It's unclear to me what it is exactly that you want to compare. Different sequencing runs will give different read names, so regardless of the tool you use you cannot compare individual reads across runs. Even if read names were the same (say you match reads across runs using the flow cell coord ...
written 6 days ago by dariober8.0k
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Answer: A: loop for samtools to deal with multiple files
... I think the `csh` shell doesn't support that `for loop` syntax (see for example https://www.cyberciti.biz/faq/csh-shell-scripting-loop-example/ ). I would use Bash unless you have to use csh. ...
written 15 days ago by dariober8.0k • updated 15 days ago by genomax33k
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Comment: C: How to calculate the percent of methylated cytosines.
... Maybe the OP is confused because "% methylated cytosines" could be interpreted as "% of genomic positions with a cytosine with some evidence of methylation". So if there are 10 cytosine positions in the genome and each of them has % methylation > 0, then "% methylated cytosines" = 100%. If this i ...
written 15 days ago by dariober8.0k
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Comment: C: Genome Browser suggestions
... Thanks for comments! Of course, I see what you mean about arrow keys being more intuitive. The reason for "return" after a command is to send the input string to ASCIIGenome which then it interprets it as appropriate, just like you need `ls` followed by `` at the Bash terminal. A subsequent ENTER wi ...
written 17 days ago by dariober8.0k
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Comment: C: Genome Browser suggestions
... Hi- There are a few options to navigate but they don't use the arrow keys (!). The UP and DOWN keys scroll commands like in most terminal shells. To move left and right one can use keys `f` and `b` (forward/backwards) or `+10k` and `-10k` to move 10kb forward or backwards. More on navigation [here][ ...
written 17 days ago by dariober8.0k
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Comment: C: Genome Browser suggestions
... Thanks for your comment - Feel free to drop an issue on github or a post here on biostars if you have any questions. ...
written 17 days ago by dariober8.0k
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Answer: A: Genome Browser suggestions
... Full disclosure: I'm the author of it. I wonder if [ASCIIGenome][1] is any use to you? It has a different approach from the other browsers as it is controlled via the command line, either interactively or automated (with some optimism I like to think of it as the vim of genome browsers). It displa ...
written 20 days ago by dariober8.0k
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Comment: C: Intersect vcf file and bed file
... `there is no header in the vcf file` this may well be the reason why bedtools doesn't recognise your vcf as such. Try adding a header to your vcf file. ...
written 8 weeks ago by dariober8.0k
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Comment: C: Does read counts for ATAC-seq differential detection make sense?
... I think these are valid concerns, maybe the discussion in this thread is useful https://www.biostars.org/p/195689/ ...
written 9 weeks ago by dariober8.0k
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Comment: C: reading txt file
... I can reproduce the problem in your original question but not the one here in the comment: my_data<- data.frame(x= c(2, 3, 1, 'x', 'y')) my_data[1,1] < 3 # Give NA and Warning d<- as.numeric(my_data[1,1]) # -> d= 2 d < 3 # -> TRUE ...
written 9 weeks ago by dariober8.0k

Latest awards to dariober

Great Question 14 days ago, created a question with more than 5,000 views. For Add read group to header after samtools merge
Teacher 17 days ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Commentator 28 days ago, created a comment with at least 3 up-votes. For C: Filtration Of Reads With Length Lower Than 30 From Bam
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Student 7 weeks ago, asked a question with at least 3 up-votes. For ChIP-Seq: Calling peaks with replicates
Appreciated 8 weeks ago, created a post with more than 5 votes. For A: Output the color code according to number
Scholar 8 weeks ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: count the number of transcription factor binding sites
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
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
Scholar 3 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Great Question 3 months ago, created a question with more than 5,000 views. For Add read group to header after samtools merge
Scholar 4 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: count the number of transcription factor binding sites
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Popular Question 5 months ago, created a question with more than 1,000 views. For Java Samtools Api: Write Bam To Stdout
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Scholar 5 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Teacher 6 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
Popular Question 7 months ago, created a question with more than 1,000 views. For Picard API: Modify sam header

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