User: xiaoleiusc
xiaoleiusc • 40
- 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
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... 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
xiaoleiusc • 40
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... thanks. Just did, works great!! ...
written 12 weeks ago by
xiaoleiusc • 40
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... 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 ...
written 12 weeks ago by
xiaoleiusc • 40
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... 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
xiaoleiusc • 40
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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
xiaoleiusc • 40
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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
xiaoleiusc • 40
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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
xiaoleiusc • 40
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... 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 ...
written 3 months ago by
xiaoleiusc • 40
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Comment:
C: HIV : gtf or gff annotation
... the link is not working anymore ...
written 3 months ago by
xiaoleiusc • 40
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... 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 ...
written 3 months ago by
xiaoleiusc • 40
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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