User: dariober

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Posts by dariober

<prev • 679 results • page 1 of 68 • next >
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Answer: A: Count mismatchs/Indel number per position in BAM file ?
... I think [pysamstats][1] will do the job here with something like: pysamstats -f ref.fa --type variation_strand aln.bam > aln.var.txt [1]: https://github.com/alimanfoo/pysamstats ...
written 1 day ago by dariober7.9k
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Answer: A: Stranger Things: unexpected limitations of popular tools
... This may be a question in itself but maybe it fits well in this thread... What's the purpose of the [SRA][1] format? Every question about it seems to be about converting from sra to fastq which makes me wonder whether the sra format was at all necessary. (Then of course, in hindsight it's easy to ...
written 5 days ago by dariober7.9k
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Answer: A: Print header of bam file using htsjdk library
... I think you should replace `rec.getHeader()` with: rec.getHeader().getTextHeader() ...
written 9 days ago by dariober7.9k
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Answer: A: cutadapt error while performing Trim_Galore
... >FASTQ file is expected to start with '@', but found '\n' If this is true It seems you have an empty line in your fastq. Try to locate it with: grep -A 10 -B 10 -n '^$' myreads.fastq This could help finding out what happened ...
written 26 days ago by dariober7.9k
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Comment: C: tabix for ID column
... Is `join` going to be faster then a sequential scan using e.g. `grep rs1234` or `grep -f rsid.txt`? ...
written 27 days ago by dariober7.9k
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Answer: A: tabix for ID column
... You could put your table in a sqlite database and index the ID column. Then retrieving records by ID will be very fast. However, this would require working with a sqlite file and associated SQL syntax rather than with the usual unix/R/python tools. ...
written 27 days ago by dariober7.9k
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Comment: C: Increase the fifth column ( MAPQ) value in Sam file
... Just a couple of things... You should print the sam header as it is, without incrementing the 5th column. I.e. with something like `if($0 ~ "^@") {print $0} else {...}`. Also you should check that incrementing the MAPQ doesn't make it out of bound, i.e. no more than 254 (255 meaning not available). ...
written 27 days ago by dariober7.9k
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Comment: C: samtools view region
... > it does not matter which end is obtained by the given list of intervals Exactly, so if the start of an interval (a read) is outside the interval, the OP wants to reject it. The OP wants to keep reads whose start is inside the interval. So if the read has start and end coordinates chr1:5-20 and ...
written 29 days ago by dariober7.9k
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Comment: C: samtools view region
... It says you can use bam as input, but you can't tell bedtools to output a read if the start is inside a target interval. If a read starts before the interval and ends somewhere inside or after the interval, bedtools will print it. The OP wants to discard such reads instead. Did I get it right? ...
written 29 days ago by dariober7.9k
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Answer: A: samtools view region
... Would this work, without resorting on additional third party tools? samtools view aln.bam X:100-1000 | awk -v FS='\t' '$4 >= 100 && $4 <= 1000' If you want also the bam header: samtools view -h aln.bam X:100-1000 | awk -v FS='\t' '$1 ~ "^@" || ($4 >= 100 && $4 &l ...
written 29 days ago by dariober7.9k

Latest awards to dariober

Good Answer 27 days ago, created an answer that was upvoted at least 5 times. For A: count the number of transcription factor binding sites
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: Filtration Of Reads With Length Lower Than 30 From Bam
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Scholar 5 weeks ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Great Question 6 weeks ago, created a question with more than 5,000 views. For Add read group to header after samtools merge
Scholar 8 weeks ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For A: count the number of transcription factor binding sites
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Popular Question 3 months ago, created a question with more than 1,000 views. For Java Samtools Api: Write Bam To Stdout
Teacher 3 months 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
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
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Commentator 4 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 5 months ago, created a question with more than 1,000 views. For Picard API: Modify sam header
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Appreciated 6 months ago, created a post with more than 5 votes. For A: Output the color code according to number
Good Question 6 months ago, asked a question that was upvoted at least 5 times. For When and why is bwa aln better then bwa mem?
Appreciated 6 months ago, created a post with more than 5 votes. For A: Output the color code according to number
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Teacher 7 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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