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Recent Replies
Comment: Extracting only soft/hard clipped reads from a bam file
by
d-cameron
★
2.7k
If you want multithreaded I/O the command-line is a pretty annoying (since you're running a tool within gridss, not the whole pipeline): yo…
Answer: Extracting only soft/hard clipped reads from a bam file
by
d-cameron
★
2.7k
Have you considered using a SV breakpoint calling tool (using a reference that includes both host and viral sequence), or a viral integrati…
Answer: Reads mapping to pseudogenes using RSubread
by
Gordon Smyth
★
5.0k
There isn't anything in your post to suggest that subread is missing FTH1 or it's exons. If these reads match the pseudogene region even sl…
Comment: Asking for introduction of a database
by
mohamadzare6022
•
0
Thank you for your suggestion;
I used the STRING database and LEM (eukaryotic linear motifs).
My protein has different Motifs and Domains …
Answer: Converting PLINK binary files into python dataframe
by
Istvan Albert
94k
Pandas is notoriously slow at reading in large datasets
I would recommend an alternative like polars or datatable:
* https://github.com/p…
Comment: Error in converting vcf file to plink format
by
Madhawa
▴
10
Thank you so much! Will try to run the analysis with the file and check it! Thanks again!!
Comment: Error in converting vcf file to plink format
by
GenoMax
120k
As long as the file is not empty it should be good.
Comment: Error in converting vcf file to plink format
by
Madhawa
▴
10
____________________________________________
I just tried with plink 1.9 and it worked pretty well!!!! Thank you once again!
Comment: Error in converting vcf file to plink format
by
Madhawa
▴
10
Thank you so much for your reply with clarification. I will try with plink 1.9!
Comment: Error in converting vcf file to plink format
by
chrchang523
9.7k
This error is a consequence of using plink 1.07, which has to load the entire dataset into memory, instead of plink 1.9, which is capable o…
Comment: Error in converting vcf file to plink format
by
Madhawa
▴
10
Thank you so much! I just check my workinf directory with "ls" and I was able to find the file name "20100804.All.panel". Does this means i…
Comment: Asking for introduction of a database
by
GenoMax
120k
While you wait on other answers start here: https://string-db.org/
Comment: Error in converting vcf file to plink format
by
GenoMax
120k
Correct. This looks like a problem with your local network. I was able to access the link without problems.
Comment: Error in converting vcf file to plink format
by
Madhawa
▴
10
Thank you for your information. I just tried with your command and got the error as Temporary failure in name resolution. Did you mean like…
Comment: Error in converting vcf file to plink format
by
GenoMax
120k
Try
wget -O 20100804/20100804.ALL.panel http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20100804/20100804.ALL.panel
If you continue…
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