User: xiaoleiusc

gravatar for xiaoleiusc
xiaoleiusc70
Reputation:
70
Status:
Trusted
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

<prev • 57 results • page 1 of 6 • next >
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Comment: C: convert DNA FASTA file to RNA FASTA file
... Hi, Mensur, Thank you very much for introducing the esl-reformat. Xiao ...
written 8 days ago by xiaoleiusc70
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Comment: C: convert DNA FASTA file to RNA FASTA file
... Hi, JC, Your Perl script works well! Thanks. Xiao ...
written 8 days ago by xiaoleiusc70
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Comment: C: convert DNA FASTA file to RNA FASTA file
... 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 xiaoleiusc70
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convert DNA FASTA file to RNA FASTA file
... 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 ...
sequence chip-seq rna-seq written 8 days ago by xiaoleiusc70 • updated 8 days ago by JC12k
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Comment: C: chipseq -- annotate peaks with lncRNA
... 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 xiaoleiusc70
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Comment: C: R error: could not find function "makeTxDbFromUCSC"
... 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 xiaoleiusc70
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R error: could not find function "makeTxDbFromUCSC"
... 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 ...
R rna-seq written 15 days ago by xiaoleiusc70
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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 xiaoleiusc70
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Comment: C: PARalyzer error: * is not found in the .2bit file
... 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 xiaoleiusc70 • updated 10 weeks ago by Ram32k
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Comment: C: Bowtie alignment run too long and not finishing job
... 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 xiaoleiusc70

Latest awards to xiaoleiusc

Voter 15 days ago, voted more than 100 times.
Teacher 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
Supporter 13 months ago, voted at least 25 times.

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