User: xiaoleiusc

gravatar for xiaoleiusc
xiaoleiusc20
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 >
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Answer: A: IGV viewer could not display genome sequences correctly
... 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 xiaoleiusc20
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Comment: C: IGV viewer could not display genome sequences correctly
... Thanks for the input. I tried to use Picard to generate *.dict file, but the problem still exists. ...
written 5 weeks ago by xiaoleiusc20
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Comment: C: IGV viewer could not display genome sequences correctly
... Thanks for the input. I have *.fasta and *.fai files, but no *.dict file. ...
written 5 weeks ago by xiaoleiusc20
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IGV viewer could not display genome sequences correctly
... 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 ) ...
rna-seq written 5 weeks ago by xiaoleiusc20
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Comment: C: How to Check Per Base Sequence Content of a Fasta file
... 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 xiaoleiusc20
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Comment: C: How to Check Per Base Sequence Content of a Fasta file
... Thanks, it seems this option is only for command line, not in the GUI of FastQC ...
written 5 weeks ago by xiaoleiusc20
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Comment: C: How to Check Per Base Sequence Content of a Fasta file
... 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 xiaoleiusc20
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Comment: C: How to Check Per Base Sequence Content of a Fasta file
... 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 xiaoleiusc20
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How to Check Per Base Sequence Content of a Fasta file
... 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 ...
rna-seq written 5 weeks ago by xiaoleiusc20
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How to set up quality filter which only applies to the 5' end of reads
... 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 ...
clip-seq chip-seq rna-seq written 4 months ago by xiaoleiusc20

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.

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