Moderator: genomax
genomax ♦ 62k
- Reputation:
- 61,760
- Status:
- Trusted
- Location:
- United States
- Last seen:
- 56 minutes ago
- Joined:
- 3 years, 8 months ago
- Email:
- g*******@gmail.com
Posts by genomax
<prev
• 11,117 results •
page 1 of 1112 •
next >
1
vote
1
answer
59
views
1
answers
... Official BBMap repo is [located here][1]. Reformat is a versatile utility that does a ton of other things. You can [find a guide here][2]. It is part of a much bigger BBTools package.
[1]: https://sourceforge.net/projects/bbmap/
[2]: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-gui ...
written 53 minutes ago by
genomax ♦ 62k
1
vote
1
answer
59
views
1
answers
... > the fastq files are not in this format
That is easily fixed using `reformat.sh` from BBMap suite.
reformat.sh in=R1.fq.gz out=R1.fa
On a serious note you could also look at this: https://digibio.blogspot.com/2017/12/nucleotide-base-frequency-per-read-and.html ...
written 2 hours ago by
genomax ♦ 62k
0
votes
1
answer
59
views
1
answers
... Is this TCGA data?
You can may be able to use `reformat.sh` from BBMap suite if all you need to do is to reformat the `/1` id's to ones that contain `:`.
spaceslash=t Put a space before the slash in addslash mode.
addcolon=f Append ' 1:' and ' 2:' to read names, i ...
written 7 hours ago by
genomax ♦ 62k
1
vote
1
answer
55
views
1
answers
... Major difference is the chemistry. NextSeq uses two color where as MiSeq users 4-color chemistry. Hopefully you have data from NextSeq v.2.5 (or what ever the new chemistry is called).
Is it ok to mix sequencing instruments in one analysis .. probably not unless you are able to introduce a batch ef ...
written 7 hours ago by
genomax ♦ 62k
0
votes
3
answers
318
views
3
answers
... Advantage of conda is that it does not need root privileges. You can install things in your own home directory. See this guide: https://www.biostars.org/p/335903/
No sudo should be needed. ...
written 1 day ago by
genomax ♦ 62k
0
votes
3
answers
318
views
3
answers
... You need to download conda and install into your account on server at school. Then things you install via conda will then live in your personal space on the server. ...
written 1 day ago by
genomax ♦ 62k
0
votes
0
answers
65
views
0
answers
... https://www.biostars.org/u/37217/ Use these directions: https://www.biostars.org/p/309884/ ...
written 1 day ago by
genomax ♦ 62k
0
votes
0
answers
65
views
0
answers
... Have you looked at "Formatting options" and then under "Other reports" clicked on "Taxonomy report"? You should see something like this.
...
written 1 day ago by
genomax ♦ 62k
0
votes
0
answers
65
views
0
answers
... What did you blast against? At NCBI or local? If local, did you get the taxonomy database file, if you downloaded pre-made indexes from NCBI. ...
written 1 day ago by
genomax ♦ 62k
0
votes
0
answers
143
views
0
answers
... There are no wrongs. You may want to use imgbb image hosting provider as shown in instructions above in future. I can't see the image you posted above perhaps others can. ...
written 1 day ago by
genomax ♦ 62k
Latest awards to genomax
Teacher
6 days ago,
created an answer with at least 3 up-votes.
For C: Insert mutations in a reference genome from a vcf
Teacher
6 days ago,
created an answer with at least 3 up-votes.
For C: Insert mutations in a reference genome from a vcf
Scholar
6 days ago,
created an answer that has been accepted.
For C: Insert mutations in a reference genome from a vcf
Commentator
22 days ago,
created a comment with at least 3 up-votes.
For C: merge Fastq or Bam file?
Teacher
23 days ago,
created an answer with at least 3 up-votes.
For C: Have bbduk retain quality scores in output after kmer trimming
Teacher
26 days ago,
created an answer with at least 3 up-votes.
For C: Have bbduk retain quality scores in output after kmer trimming
Scholar
29 days ago,
created an answer that has been accepted.
For C: Have bbduk retain quality scores in output after kmer trimming
Scholar
4 weeks ago,
created an answer that has been accepted.
For C: Have bbduk retain quality scores in output after kmer trimming
Teacher
4 weeks ago,
created an answer with at least 3 up-votes.
For C: Have bbduk retain quality scores in output after kmer trimming
Popular Question
4 weeks ago,
created a question with more than 1,000 views.
For Synthetic DNA/RNA Spike-in standards for NGS
Teacher
4 weeks ago,
created an answer with at least 3 up-votes.
For C: Have bbduk retain quality scores in output after kmer trimming
Scholar
5 weeks ago,
created an answer that has been accepted.
For C: Have bbduk retain quality scores in output after kmer trimming
Commentator
5 weeks ago,
created a comment with at least 3 up-votes.
For C: merge Fastq or Bam file?
Commentator
5 weeks ago,
created a comment with at least 3 up-votes.
For C: merge Fastq or Bam file?
Teacher
5 weeks ago,
created an answer with at least 3 up-votes.
For C: Have bbduk retain quality scores in output after kmer trimming
Scholar
5 weeks ago,
created an answer that has been accepted.
For C: Have bbduk retain quality scores in output after kmer trimming
Scholar
5 weeks ago,
created an answer that has been accepted.
For C: Have bbduk retain quality scores in output after kmer trimming
Scholar
6 weeks ago,
created an answer that has been accepted.
For C: Have bbduk retain quality scores in output after kmer trimming
Scholar
6 weeks ago,
created an answer that has been accepted.
For C: Have bbduk retain quality scores in output after kmer trimming
Good Answer
6 weeks ago,
created an answer that was upvoted at least 5 times.
For C: Repeat masker bed file
Commentator
6 weeks ago,
created a comment with at least 3 up-votes.
For C: merge Fastq or Bam file?
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1233 users visited in the last hour