0
votes
0
replies
34
views
0
votes
1
reply
67
views
updated 3 hours ago by
ATpoint
88k
•
written 5 hours ago by
rajdeepboral00
▴
70
0
votes
1
reply
63
views
0
votes
1
reply
74
views
1
vote
6
replies
263
views
updated 6 hours ago by
GenoMax
151k
•
written 1 day ago by
Luca Arbore
▴
10
838
votes
170
replies
178k
views
112 follow
updated 5 weeks ago by
Biostar
3.6k
•
written 8.5 years ago by
Istvan Albert
102k
1
vote
7
replies
2.3k
views
2
votes
2
replies
125
views
8 hours ago by
Andrew
•
0
1
vote
1
reply
64
views
0
votes
0
replies
57
views
10 hours ago by
Physalia-courses
★
2.6k
0
votes
0
replies
54
views
0
votes
0
replies
57
views
2
votes
1
reply
100
views
updated 13 hours ago by
Mensur Dlakic
★
29k
•
written 14 hours ago by
marongiu.luigi
▴
740
0
votes
0
replies
63
views
0
votes
0
replies
59
views
15 hours ago by
this_is_me_trying
•
0
1
vote
2
replies
128
views
updated 11 hours ago by
GenoMax
151k
•
written 16 hours ago by
genomics_student
•
0
0
votes
3
replies
676
views
0
votes
3
replies
384
views
0
votes
1
reply
272
views
updated 17 hours ago by
agis.maulana12
•
0
•
written 5 days ago by
Wenhai
•
0
3
votes
4
replies
203
views
updated 1 day ago by
GenoMax
151k
•
written 1 day ago by
anthony.santana.703.j
▴
30
0
votes
1
reply
146
views
updated 1 day ago by
LChart
4.9k
•
written 1 day ago by
ton_of_questions
•
0
2
votes
2
replies
437
views
updated 1 day ago by
this_is_me_trying
•
0
•
written 3 months ago by
lijiangres
▴
20
7
votes
6
replies
279
views
updated 1 day ago by
colindaven
7.5k
•
written 1 day ago by
SomeOne
▴
180
0
votes
1
reply
214
views
updated 1 day ago by
shenwei356
8.7k
•
written 2 days ago by
curiousfellow@123
•
0
7
votes
2
replies
410
views
updated 1 day ago by
colindaven
7.5k
•
written 7 days ago by
anna
▴
70
2
votes
1
reply
217
views
updated 1 day ago by
Mensur Dlakic
★
29k
•
written 2 days ago by
Rushikesh
▴
10
7
votes
7
replies
2.2k
views
6 follow
0
votes
2
replies
648
views
5
votes
9
replies
675
views
0
votes
0
replies
139
views
0
votes
2
replies
194
views
1 day ago by
J.F.Jiang
▴
930
2
votes
2
replies
215
views
16 hours ago by
Mark
▴
50
5
votes
2
replies
376
views
0
votes
4
replies
265
views
updated 2 days ago by
Michael
55k
•
written 2 days ago by
María José
▴
10
0
votes
2
replies
193
views
14
votes
19
replies
8.2k
views
10 follow
2
votes
0
replies
201
views
0
votes
0
replies
159
views
1
vote
1
reply
235
views
9
votes
7
replies
3.0k
views
updated 4 days ago by
Damianos P. Melidis
▴
60
•
written 6.5 years ago by
DanielC
▴
210
0
votes
4
replies
521
views
0
votes
2
replies
320
views
0
votes
0
replies
875
views
updated 5 days ago by
GenoMax
151k
•
written 5 days ago by
salma.sarker
•
0
0
votes
0
replies
272
views
5 days ago by
xinguok794
•
0
5
votes
1
reply
569
views
updated 5 days ago by
LChart
4.9k
•
written 7 days ago by
anita.szabo08
▴
10
1
vote
2
replies
385
views
0
votes
3
replies
391
views
0
votes
1
reply
391
views
0
votes
1
reply
336
views
2
votes
3
replies
397
views
updated 6 days ago by
shelkmike
★
1.6k
•
written 6 days ago by
synthiiihuh
•
0
Recent Votes
Recent Locations •
All
Australia, 24 minutes ago
Ireland, 27 minutes ago
United States, 31 minutes ago
Ghana, 36 minutes ago
São Paulo, 36 minutes ago
USA, 38 minutes ago
Namibia, 44 minutes ago
Recent Awards •
All
Popular Question to
ssko
▴
20
Popular Question to
Physalia-courses
★
2.6k
Popular Question to
i.sudbery
21k
Popular Question to
marongiu.luigi
▴
740
Popular Question to
debitboro
▴
270
Recent Replies
Answer: GSEA analysis in R
by
ATpoint
88k
It doesn't matter really. Both shrunken logFCs and test statistics are fine and there is no real justification of one over the other. This …
Comment: ATAC-seq analysis
by
GenoMax
151k
Name sorting would be essential only if you were converting a BAM to fastq reads or marking duplicates. To visualize the data position sort.
Comment: Assembly issues
by
GenoMax
151k
Please post `galaxy` related help questions on their help forum for prompt response: https://help.galaxyproject.org/
They can see your dat…
Comment: Use taxdb tp get scientific names in local BLAST output
by
GenoMax
151k
> Do I need to get the taxids in a different way in this case?
Yes. You can get the accession to taxID mapping file from https://ftp.ncbi.…
Comment: is there a way to get SRA info (Paired Library, Sample id, Seq Tech... etc) usin
by
Wayne
★
2.1k
Tagging this with a comment because the expansive title of the original question makes this feature prominently in search results...
Ther…
Comment: Use taxdb tp get scientific names in local BLAST output
by
Luca Arbore
▴
10
Thank you very much Genomax. Now, because there may be a misunderstanding I need to clarify the following:
I do not have the nt database d…
Answer: Search all SRA data for sequence? Raw reads only
by
Wayne
★
2.1k
There's now [Logan Search](https://logan-search.org/). (presently it covers through the end of 2023)
>"Given a DNA sequence, the service…
Comment: Is this Rosalind inspired project actually useful?
by
Andrew
•
0
Thanks for the reply!
It definitely has been useful on a personal level to grow the functionality of this for my specific use case because…
Answer: Is this Rosalind inspired project actually useful?
by
jared.andrews07
★
18k
That functionality can be found in [biopython](https://biopython.org/wiki/Documentation), which is the most general bioinformatics toolkit …
Answer: Subset a GAM (graph alignment) file
by
glenn.hickey
▴
530
For the first 1000 reads:
```
vg view -a myreads.gam | head -n1000 | vg view -a -G -J - > myreads_1000.gam
```
For downsampling like …
Answer: Use taxdb tp get scientific names in local BLAST output
by
GenoMax
151k
With `blast+ v.2.16`.
Get the sequences for `diptera` from "nt" blast db.
$ blastdbcmd -db nt -taxids 7147 -outfmt %f > test.fa
Whil…
Comment: Still bad phred score after fastp
by
Arup Ghosh
3.3k
By default, the quality score threshold is `15`. So if you have not specified a value for `--qualified_quality_phred` or `--average_qual`, …
Comment: Server Requirements for long read data analysis
by
GenoMax
151k
EPI2ME workflows available from ONT for sake of completeness: https://nanoporetech.com/products/analyse/epi2me
A number of pre-made NF wor…
Answer: How to automate blasting contigs?
by
Mensur Dlakic
★
29k
There is nothing to automate if all the contigs are in a single file.
blastn -query contigs.fna -db nr -task blastn -out contigs_vs_nr…
Comment: Use taxdb tp get scientific names in local BLAST output
by
Luca Arbore
▴
10
Thank you for replies. Fast headers of downloaded sequences look like this
grep "^>" diptera_coi_030625.fasta | head -n 5
>AB0…
Traffic: 2387 users visited in the last hour
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by the
version 2.3.6
version 2.3.6