User: fitziano

gravatar for fitziano
fitziano40
Reputation:
40
Status:
New User
Location:
Switzerland
Last seen:
8 months, 2 weeks ago
Joined:
6 years, 4 months ago
Email:
f*****@gmail.com

Posts by fitziano

<prev • 4 results • page 1 of 1 • next >
3
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1
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2.3k
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Answer: A: bedtools multicov and fraction overlap flag
... At the end, what I found out is that the -f flag in bedtools multicov refers to the bed file. So the solution to this is to first filter the alignment files with bedtools intersect: bedtools intersect -f 1 -s -abam file1.bam -b introns.bed > filter1.bam and then run the bedtools multicov like ...
written 5.7 years ago by fitziano40
0
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1
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Comment: C: bedtools multicov and fraction overlap flag
... Yes. If I don't use the -f flag, reads are reported. But I get also reads that occur between exons and introns. ...
written 5.7 years ago by fitziano40
3
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1
answer
2.3k
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1
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bedtools multicov and fraction overlap flag
... I am trying to use bedtools multicov to count the reads that map to introns. For this I have constructed a bed6 file containing the intronic regions. The problem is that I want to keep only reads that completely map to intronic regions (no splice junctions/ no exonic reads). For this I run bedtool ...
bedtools rna-seq written 5.7 years ago by fitziano40
8
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Tool that detects data types
... Hi guys I am looking for a tool that is able to automatically detect and validate type of a file. More specifically I am interested for detecting between SAM, BAM, FASTA, FASTQ (if possible descriminating between these types), BED, BED12, BED15, GFF, GFF2, GFF3. The detection should be performed ...
data type tool rna-seq written 6.4 years ago by fitziano40 • updated 6.4 years ago by Pierre Lindenbaum133k

Latest awards to fitziano

Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: bedtools multicov and fraction overlap flag
Popular Question 3.7 years ago, created a question with more than 1,000 views. For bedtools multicov and fraction overlap flag
Popular Question 4.9 years ago, created a question with more than 1,000 views. For Tool that detects data types

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