User: Arko
Arko • 30
- Reputation:
- 30
- Status:
- New User
- Location:
- US/Boston/Boston University
- Last seen:
- 1 year, 1 month ago
- Joined:
- 2 years, 7 months ago
- Email:
- a*****@bu.edu
Posts by Arko
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... I'm working with 4 samples (10x sequenced) and loading them into Seurat using the Read10x() function to read them in and then using the merge() function to combine them into 1 object.
But on doing this, each sample is given a sample ID given to it based on the origin of the data.
While running PCA ...
written 13 months ago by
Arko • 30
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... I plan on doing that soon, thought I'd see if the community would have any suggestions first. Thanks! ...
written 15 months ago by
Arko • 30
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... I'm working with whole exome sequencing data from mouse (mm9) in the fastq format.
I have an interval list for the sequencing data as well and I want to obtain VCF files from each sample, using GATK best practices on Terra Bio but GATK best practices are tailored to only to human data, so all the WD ...
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... I was hoping it wouldn't come to that, altering source code always ends up breaking it. At least in my case. Thanks though! ...
written 16 months ago by
Arko • 30
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... I'm experimenting with CPCA made available in the contrastive module in python.
Description found here - https://www.nature.com/articles/s41467-018-04608-8#Bib1
GitHub and Description here - https://github.com/abidlabs/contrastive
I'm trying to obtain the eigenvalues (loadings) for the CPCA run, ...
written 16 months ago by
Arko • 30
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... Good idea, I shall have a look at it! ...
written 18 months ago by
Arko • 30
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... 6AAAAEEEEEEEEEEEEEEEE////A
@NS500496_727_H373LBGXB:2:23203:12170:5855#AGAATAAAAGAGTGAT/1
GAGGAAGTTCCAGCCAAGGAGATTGA
+NS500496_727_H373LBGXB:2:23203:12170:5855#AGAATAAAAGAGTGAT/1
AAAAAEEAEE/AEEAAEEAEE//E/<
@NS500496_727_H373LBGXB:2:23203:1526:5855#ACATCATCCCGAGTGG/1
CAG ...
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... Hi!
I'm trying to read in a fastQ file and carry out some operations on it (Demultiplexing the file into various fastq files based on exact matching barcodes)
Midway through the fastQ file, I'm getting the following error :
ValueError: End of file without quality information.
try:
...
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Comment:
C: Querying VEP using REST API
... All fields into a tsv or a csv format preferably. Something that's easy to read. Right now it's a mess when outputting into a text file directly. ...
written 2.1 years ago by
Arko • 30
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