User: xiaoleiusc

gravatar for xiaoleiusc
xiaoleiusc40
Reputation:
40
Status:
New User
Location:
USA/New York/The Rockefeller University
Last seen:
2 months, 3 weeks ago
Joined:
1 year ago
Email:
x*********@gmail.com

Posts by xiaoleiusc

<prev • 38 results • page 1 of 4 • next >
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Comment: C: Parameters That Determine Meme Speed And Homer Speed For Motif Discovery?
... Hi, Ryan, I found that MEME-chip requires equal-length nucleotide sequences to be analyzed (http://meme-suite.org/tools/meme-chip). However, a bed file format containing identified clusters from my CLIP experiment are not equal length (e.g. 30 to 50 bp in one of my sample and 30 to 300bp in another ...
written 12 weeks ago by xiaoleiusc40
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Comment: C: Why bowtie report same number of reads with different - k parameters?
... thanks. Just did, works great!! ...
written 12 weeks ago by xiaoleiusc40
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Why bowtie report same number of reads with different - k parameters?
... Hi, All, I use bowtie to align my short RNA reads to the hg19 genome. I tested different ways of reporting alignment read number by changing -k parameter, however, I found bowtie report the number of aligned reads even with different -k parameters. This behavior of bowtie is also inconsistent with ...
clip-seq rna-seq written 12 weeks ago by xiaoleiusc40
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Comment: C: How to get multi mappers from bowtie 1
... Hi Carlo, Thanks for your answer, but all my short RNA reads from bowtie 1 does not have mapping quality score (all of them have 255). In addition, there is no NH value in the output sam file. ...
written 12 weeks ago by xiaoleiusc40
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Comment: C: GTF file for HIV strain pNL4-3
... Hi, caggtaagtat , I wonder if your HIV NL4-3 GFF/GTF file works? I have the same question and I could not find GFF/GTF of NL4-3 despite intensive google search. Best, Xiao ...
written 3 months ago by xiaoleiusc40
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Comment: C: GTF/GFF for non-coding RNA
... Hi, Igor, I followed your instructions and downloaded the hg19_gtf, but there is not "gene_biotype" column in the gtf (screen capture link: https://drive.google.com/file/d/1OkpcDF_u2-yzAKlg8s46vIVOi8pc4AZ1/view?usp=sharing) ...
written 3 months ago by xiaoleiusc40
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Comment: C: get gene biotype for hg38 refseq
... Hi vkkodali, I have the same question, I followed your answer and download hg19_gtf file but in column 9, there is only gene id, not gene_biotype (screen capture link: https://drive.google.com/file/d/1OkpcDF_u2-yzAKlg8s46vIVOi8pc4AZ1/view?usp=sharing ) ...
written 3 months ago by xiaoleiusc40
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HIV NL4-3 transcriptome fasta
... Hi, All, I wonder is there a place which I can download HIV NL4-3 transcriptome Fasta file as a reference file in my NGS RNA reads mapping? Although I know how to use the HIV NL4-3 genome as a reference file, however, I am particularly interested in the reads that are generated from HIV RNA splic ...
clip-seq rna-seq written 3 months ago by xiaoleiusc40
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Comment: C: HIV : gtf or gff annotation
... the link is not working anymore ...
written 3 months ago by xiaoleiusc40
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how to annotate cluster file which is not .bed format
... Dear All, I run Paralyzer to process my PAR-CLIP data and the output cluster file is a .csv file which looks like below (or please see screenshot https://drive.google.com/file/d/1UhcJXHNYavKDA7LdusYaV7QTbN8g1kG-/view?usp=sharing): Chromosome Strand ClusterStart ClusterEnd ClusterID ClusterSequence ...
rna-seq; clip-seq written 3 months ago by xiaoleiusc40

Latest awards to xiaoleiusc

Scholar 5 months ago, created an answer that has been accepted. For A: IGV viewer could not display genome sequences correctly
Supporter 5 months ago, voted at least 25 times.

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