Moderator: Alex Reynolds
Alex Reynolds ♦ 25k
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- Seattle, WA USA
- Website:
- http://dropbit.com/
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- AlexReynolds
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- Last seen:
- 6 hours ago
- Joined:
- 8 years, 9 months ago
- Email:
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One of the developers behind the fast BEDOPS suite, whose pug Zac is the bestest pug in the world.
Posts by Alex Reynolds
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Comment:
C: Illegal Division by zero
... Debug the values of the array at different stages of the script. Check that the array is initialized to non-zero values, or that a pseudocount is applied correctly. ...
written 2 days ago by
Alex Reynolds ♦ 25k
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... You could use Python `mygene` with the `ensembl.transcript` scope:
#!/usr/bin/env python
import sys
import mygene
mg = mygene.MyGeneInfo()
names = []
for line in sys.stdin:
names.append(line.rstrip())
for name in names:
result = mg.que ...
written 7 days ago by
Alex Reynolds ♦ 25k
0
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1
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... If `A.bed` is your narrowPeak file:
$ awk -vOFS="\t" -vFS="\t" '{ print $1, $2, $3, $4"%%"$10 }' A.bed > A.custom.bed
The ID of `A.custom.bed` contains the original peak ID, concatenated with the summit position, using `%%` as a delimiter.
Repeat for peak files `B.bed` and `C.bed`.
Once y ...
written 7 days ago by
Alex Reynolds ♦ 25k
0
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1
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... Okay, your input is a little different than I assumed.
Perhaps try a regular expression, instead:
$ for gene in `cat genes.txt`; do bedops --intersect A.bed <(awk -vgene=${gene} -vOFS="\t" -vFS="\t" '{ regex = "^"gene; if ($4 ~ regex) { print $0; } }' B.bed) | awk -vgene=${gene} -vOFS="\t" ...
written 8 days ago by
Alex Reynolds ♦ 25k
0
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1
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... Can you do the same for `A.bed` and `B.bed`:
$ cat -te A.bed | head
...
$ cat -te B.bed | head
...
I'm reviewing things and I'm not sure what's wrong. ...
written 8 days ago by
Alex Reynolds ♦ 25k
0
votes
1
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135
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... What happens if you run:
$ for gene in `cat genes.txt`; do echo ${gene}; done
Also, do you have any weird line endings in `genes.txt`? Perhaps copy and paste the output from running this so we can take a look:
$ cat -te genes.txt | head ...
written 8 days ago by
Alex Reynolds ♦ 25k
0
votes
1
answer
135
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1
answers
... Are you using the built-in `awk` on OS X? If so, you might use Homebrew to install GNU awk: `brew install awk`. ...
written 8 days ago by
Alex Reynolds ♦ 25k
1
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1
answer
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1
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... Use `awk` to grab the summit column from a peak file and put it into the ID field (fifth column):
$ awk '{ print ... }' A > A.custom
Repeat for inputs B and C.
Map the merged custom intervals to the customized intervals, to get the IDs contained with the merged interval:
$ bedmap --ec ...
written 8 days ago by
Alex Reynolds ♦ 25k
0
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Comment:
C: How to color subset of row ?
... Hello Björn!
We believe that this post does not fit the main topic of this site.
This is not a bioinformatics question. You might ask on Stack Overflow.
For this reason we have closed your question. This allows us to keep the site focused
on the topics that the community can help with.
If you ...
written 8 days ago by
Alex Reynolds ♦ 25k
3
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1
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1
answers
... Assuming five-column BED, with the score or signal in the fifth column:
$ awk '$5>100' in.bed > out.bed
If you're working with a bedGraph file:
$ awk '$4>100' in.bedGraph > out.bedGraph ...
written 9 days ago by
Alex Reynolds ♦ 25k
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