User: xiaoleiusc
xiaoleiusc • 20
- Reputation:
- 20
- Status:
- New User
- Location:
- USA/New York/The Rockefeller University
- Last seen:
- 2 weeks ago
- Joined:
- 7 months, 4 weeks ago
- Email:
- x*********@gmail.com
Posts by xiaoleiusc
<prev
• 23 results •
page 1 of 3 •
next >
2
votes
1
answer
146
views
1
answers
... Thanks all for the inputs. Igv developer solved the problem, I pasted the solution here:
OK, the problem is your fasta file is missing a line feed at the end of the file. This is a problem because the index (fai) file says there are 9179 bases, and 9180 bytes in each line. So that last byte (th ...
written 5 weeks ago by
xiaoleiusc • 20
0
votes
1
answer
146
views
1
answers
... Thanks for the input. I tried to use Picard to generate *.dict file, but the problem still exists. ...
written 5 weeks ago by
xiaoleiusc • 20
0
votes
1
answer
146
views
1
answers
... Thanks for the input. I have *.fasta and *.fai files, but no *.dict file. ...
written 5 weeks ago by
xiaoleiusc • 20
3
votes
1
answer
146
views
1
answer
... Dear All,
Although I updated my IGV viewer to the newest version (2.8) in my MacOS, it could not display genome sequences correctly, it displays each base in the sequence as little squares at the bottom " sequence" track.
I attach a screenshot here ( https://photos.app.goo.gl/Vn2wtDgkh1xhgufR7 ) ...
written 5 weeks ago by
xiaoleiusc • 20
0
votes
0
answers
138
views
0
answers
... I located the FastQC app on my MacOS, right click show package content, and do ./fastqc --nogroup, it works great. Thanks a lot Genomax! ...
written 5 weeks ago by
xiaoleiusc • 20
0
votes
0
answers
138
views
0
answers
... Thanks, it seems this option is only for command line, not in the GUI of FastQC ...
written 5 weeks ago by
xiaoleiusc • 20
0
votes
0
answers
138
views
0
answers
... Thanks, I see. I could look for a tool to add fake qualities. But I noticed that in FastQC, the tool could give you "per base content" of a short read (say in my example, the read length is 36 bp), if I have a long read (say 75 bp single read), the FastQC only give me "per base content" of each base ...
written 5 weeks ago by
xiaoleiusc • 20
0
votes
0
answers
138
views
0
answers
... Thanks, It's a fasta file from Illumina sequencing but without quality data (processed fastq file, pcr duplications are collapsed). ...
written 5 weeks ago by
xiaoleiusc • 20
2
votes
0
answers
138
views
0
answers
... Hi All,
What tool or program should I run to check "Per Base Sequence Content " of a fasta format file from NGS sequencing ? I know FastQC could check "Per Base Sequence Content " of a fastq file, but unfortunately FastQC does not take a fasta format as input.
Thanks ahead,
Xiao
Image link of ...
written 5 weeks ago by
xiaoleiusc • 20
0
votes
0
answers
191
views
0
answers
... Hi, All,
I have a question of how to set up a quality filter which only applies to the first 3 bases at 5' ends of my reads. I want to set up a threshold (i.e. Quality score 20) so that if any reads in my input FASTQ file which have any of the first 3 bases below the threshold will be discarded or ...
written 4 months ago by
xiaoleiusc • 20
Latest awards to xiaoleiusc
Scholar
5 weeks ago,
created an answer that has been accepted.
For A: IGV viewer could not display genome sequences correctly
Supporter
5 weeks ago,
voted at least 25 times.
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1454 users visited in the last hour