User: xiaoleiusc
xiaoleiusc • 70
- Reputation:
- 70
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- Location:
- USA/New York/The Rockefeller University
- Last seen:
- 4 days, 7 hours ago
- Joined:
- 1 year, 8 months ago
- Email:
- x*********@gmail.com
Posts by xiaoleiusc
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... Hi, Mensur,
Thank you very much for introducing the esl-reformat.
Xiao ...
written 8 days ago by
xiaoleiusc • 70
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... Hi, JC,
Your Perl script works well! Thanks.
Xiao ...
written 8 days ago by
xiaoleiusc • 70
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... Hi, Ram,
Sorry for the confusion. I mean changing T s to U s (not reverse complement). Basically, I have a DNA file in FASTA format, and I would like to change the T s in the DNA to U s.
Thanks.
Xiao ...
written 8 days ago by
xiaoleiusc • 70
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... Hi, All,
Is there a tool to convert a DNA FASTA file to an RNA FASTA file? I know there are online servers that could accept DNA sequences and do the conversion, however, it seems that these servers do not accept DNA FASTA files.
Thanks,
Xiao ...
written 8 days ago by
xiaoleiusc • 70
• updated
8 days ago by
JC ♦ 12k
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... Dear Dr. Yu,
Thank you very much to provide an example here. I wonder if there is a way to use ChIPseeker to summarize features including tRNAs and CDS (protein-coding sequences) from a bed file of ChIP clusters. The genomic annotation summary is similar to the example you provided here, but with f ...
written 10 days ago by
xiaoleiusc • 70
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... Hi, zx8754,
I did not load the GenomicFeatures library, after I loaded it according to your post, I could run the makeTxDbFromUCSC function in R.
I really appreciate your help.
Best,
Xiao
...
written 15 days ago by
xiaoleiusc • 70
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... Dear All,
I wonder if R stops support for "makeTxDbFromUCSC" function? I tried many times but keep failing with the error message below:
**> txDB <- makeTxDbFromUCSC(genome = "hg19", tablename = "ensGene")**
**Error in makeTxDbFromUCSC(genome = "hg19", tablename = "ensGene") :
could not ...
written 15 days ago by
xiaoleiusc • 70
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1
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Comment:
C: HIV NL4-3 transcriptome fasta
... Hi, Prisca,
Unfortunately no progress on this. I could not find a database with NL4-3 splicing transcriptome.
Best,
Xiao ...
written 27 days ago by
xiaoleiusc • 70
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... Hi, Seokju,
Sorry for the late reply but I just saw your message today. I did not include `=COLLAPSED` in my PARalyzer ini file. I use fastx_toolkit to collapse reads. Here is one of my ini file for PARalyzer below:
BANDWIDTH=3
CONVERSION=T>C
MINIMUM_READ_COUNT_PER_GROUP=10
MINI ...
written 11 weeks ago by
xiaoleiusc • 70
• updated
10 weeks ago by
Ram ♦ 32k
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... Thanks Genomax. I tried Bowtie hg19 index downloaded from iGenome and the problem solved. I also tried to index with bowtie-build of my hg19 fasta file, it also solved the problem. Somehow my bowtie index is not perfect. ...
written 6 months ago by
xiaoleiusc • 70
Latest awards to xiaoleiusc
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15 days ago,
voted more than 100 times.
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6 months ago,
created an answer with at least 3 up-votes.
For A: IGV viewer could not display genome sequences correctly
Scholar
13 months ago,
created an answer that has been accepted.
For A: IGV viewer could not display genome sequences correctly
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13 months ago,
voted at least 25 times.
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