User: fitziano
fitziano • 40
- 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
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3
votes
1
answer
2.3k
views
1
answers
... 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
fitziano • 40
0
votes
1
answer
2.3k
views
1
answers
... 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
fitziano • 40
3
votes
1
answer
2.3k
views
1
answer
... 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 ...
written 5.7 years ago by
fitziano • 40
8
votes
1
answer
2.8k
views
1
answer
... 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 ...
written 6.4 years ago by
fitziano • 40
• updated
6.4 years ago by
Pierre Lindenbaum ♦ 133k
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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