User: boczniak767
boczniak767 • 600
- Reputation:
- 600
- Status:
- Trusted
- Location:
- Poland
- Last seen:
- 1 week, 1 day ago
- Joined:
- 6 years, 10 months ago
- Email:
- m*************@protonmail.ch
Posts by boczniak767
<prev
• 124 results •
page 1 of 13 •
next >
0
votes
1
answer
74
views
1
answers
... Thanks for reply, I use version 3.5 in work and 3.6.1 on my laptop.
...
written 8 days ago by
boczniak767 • 600
0
votes
1
answer
74
views
1
answer
... Hi,
so I had a `cys` file with ca 10 big networks (ca 30k nodes each), giving a 100Mb file.
I decided to leave only three networks with max 30 (thirty) nodes to make file loading faster (much faster).
Nevertheless file size was reduced very little and the file loading takes very long.
Why is that? ...
written 10 days ago by
boczniak767 • 600
• updated
8 days ago by
scooter • 50
0
votes
3
answers
5.7k
views
3
answers
... Late answer but maybe will be helpful for someone. This generates sequence for one indyvidual at a time.
First compress your `vcf` file
`bgzip name.vcf > name.vcf.gz`
Then make an index (requred by `vcf-consensus`)
`tabix name.vcf.gz`
Finally for SC9 individual
`cat reference_genome.fa | v ...
written 7 months ago by
boczniak767 • 600
0
votes
4
answers
4.1k
views
4
answers
... I have the same error, it turns out that my bed file has positions reversed. So start coordinate was higher than stop. ...
written 10 months ago by
boczniak767 • 600
0
votes
4
answers
41k
views
4
answers
Comment:
C: Convertion Of Gff3 To Gtf
... `gffread` from Cufflinks version 2.2.1 not work properly, it leaves only "gene_id" and "transcript_id" from the 9th column. E.g. exon number was stripped. I've not used the latest version, because I couldn't find the binaries and don't want to install additional packages needed for compilation. ...
written 13 months ago by
boczniak767 • 600
0
votes
4
answers
41k
views
4
answers
Comment:
C: Convertion Of Gff3 To Gtf
... I'm not sure if this produce really **gtf**, after above commands I have "gff-version 2" in the header of exported file. ...
written 13 months ago by
boczniak767 • 600
1
vote
2
answers
822
views
2
answers
... You could also check very good one-liner solution provided in this message https://www.biostars.org/p/241744/ ...
written 13 months ago by
boczniak767 • 600
1
vote
6
answers
3.3k
views
6
answers
... I think, Probability Of Expression package could help https://rdrr.io/bioc/metaArray/man/poe.mcmc.html. ...
written 14 months ago by
boczniak767 • 600
0
votes
0
answers
382
views
0
answers
... Probe-level analysis allows you to use it later, in case your probe-gene annotation improves.
> you could use the probes as variables in your analysis although you would probably still have to deal with the high correlation between probes targeting the same transcripts.
Its true, but it also al ...
written 14 months ago by
boczniak767 • 600
0
votes
3
answers
7.7k
views
3
answers
... So, for a matrix `x` containing some rows and columns with all NAs try:
`x_no_na_col=x[,apply(!is.na(x),2,any)]` for columns
and
`ind <- apply(x_no_na_col, 1, function(x_no_na_col) all( is.na(x_no_na_col)))`
then
`x_no_na=x_no_na_col[!ind,]` for rows ...
written 14 months ago by
boczniak767 • 600
Latest awards to boczniak767
Popular Question
6 months ago,
created a question with more than 1,000 views.
For FAIRE-seq optimal coverage - large genome
Centurion
14 months ago,
created 100 posts.
Popular Question
14 months ago,
created a question with more than 1,000 views.
For [Excel 2003] Heatmap, Keep Color Only
Great Question
18 months ago,
created a question with more than 5,000 views.
For [Excel 2003] Heatmap, Keep Color Only
Teacher
21 months ago,
created an answer with at least 3 up-votes.
For A: Tools To Find Gene Ontology Term Enrichment
Popular Question
3.4 years ago,
created a question with more than 1,000 views.
For Interpro Enrichment - Any Organism
Teacher
3.4 years ago,
created an answer with at least 3 up-votes.
For A: Tools To Find Gene Ontology Term Enrichment
Popular Question
3.7 years ago,
created a question with more than 1,000 views.
For [Excel 2003] Heatmap, Keep Color Only
Popular Question
3.9 years ago,
created a question with more than 1,000 views.
For [Excel 2003] Heatmap, Keep Color Only
Popular Question
4.1 years ago,
created a question with more than 1,000 views.
For [Excel 2003] Heatmap, Keep Color Only
Teacher
4.2 years ago,
created an answer with at least 3 up-votes.
For A: Transcription Factor Enrichment
Voter
4.5 years ago,
voted more than 100 times.
Supporter
4.5 years ago,
voted at least 25 times.
Good Answer
5.7 years ago,
created an answer that was upvoted at least 5 times.
For A: Workflows For Microarray Meta-Analysis Projects.
Appreciated
5.7 years ago,
created a post with more than 5 votes.
For A: Workflows For Microarray Meta-Analysis Projects.
Teacher
5.7 years ago,
created an answer with at least 3 up-votes.
For A: Workflows For Microarray Meta-Analysis Projects.
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 748 users visited in the last hour