User: boczniak767
boczniak767 • 690
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Posts by boczniak767
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... I'm working on maize and Plant Reactome has maize IDs (version 4). So I don't have to map my genes. ...
written 4 months ago by
boczniak767 • 690
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... This happened again, not sure it is the same thing, but here is the link
[link][1]
[1]: https://dnagenics.com/admixture-ucla-human-genetics/ ...
written 7 months ago by
boczniak767 • 690
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... The problem is that the majority of data are zeros. There are no (or very few) rows (genes) with significant data for all columns (projects). Full set has ca. 10 columns, I could use smaller set of five, but the problem remains. ...
written 11 months ago by
boczniak767 • 690
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... Hi all,
I have made a table of log2 fold change ratios from several microarray studies.
For genes without statistically significant change I typed `0` (there are many such cases), other values are just log2 fold changes.
My question is, if it is possible to make clustering of such data?
I could, o ...
written 11 months ago by
boczniak767 • 690
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... Hi all,
I'm wondering if it is possible to compare MN-ase and FAIRE (or DN-ase) results.
I tried to compare it using `bedtools intersect -v` to count features shared and not-shared between files.
In theory, MN-ase gives opposite results to FAIRE or DN-ase. So great number of not shared features wo ...
written 11 months ago by
boczniak767 • 690
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... Hi all,
I'm trying the IDR procedure for FAIRE-seq peaks generated with Homer
The procedure is outlined here [homer-idr][1]
[1]: https://github.com/karmel/homer-idr#using-homer-idr
It works ok till step 5.
Using command as in example `python run_idr.py pseudoreplicate -d [tag_dirs to split] ...
written 12 months ago by
boczniak767 • 690
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... Ok, so I managed to do what I needed.
Maybe for someone it would be useful.
In short:
1. I unpacked the `cys` file and renamed to `zip`
2. In `tables` subdirectory I searched files with instances of "DAP" (the part of a columns' name, which I wanted to delete) and writeit to file `grep -rl 'DAP ...
written 15 months ago by
boczniak767 • 690
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... Check-out the Trimmomatic and `ILLUMINACLIP` function. It has a library for different TruSeq adapters which you specify in command. ...
written 15 months ago by
boczniak767 • 690
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... Hi,
I have a problem with deleting columns in one of the networks in Cytoscape file.
Formerly the session file was big, with huge network from which I separated few small.
I also used Dynet app to compare the networks and this generated new columns.
Then I deleted majority of networks to create sm ...
written 15 months ago by
boczniak767 • 690
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... It gives strange results for mean, and I don't know why. For my sam file, for 10000 lines it gives 217 (picard gives 198). This script for all reads gives 1032,79. Overall it seems that the value increases along with the read number.
Edit.
Other, smaller, file. Picard mean = 156
Qualimap and menti ...
written 16 months ago by
boczniak767 • 690
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