User: wanziyi89

gravatar for wanziyi89
wanziyi8950
Reputation:
50
Status:
New User
Location:
Singapore, Temasek Life Sciences Laboratory
Last seen:
10 months ago
Joined:
4 years, 11 months ago
Email:
w********@gmail.com

Posts by wanziyi89

<prev • 20 results • page 1 of 2 • next >
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Comment: C: Where did EMBOSS go?
... 12 months later, still saves my day! Thanks!! ...
written 3.8 years ago by wanziyi8950
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(Closed) Changing Fasta Header
... Dear Colleagues, I would like to change my FASTA file header from this : >oreNil2_augustusGene_g25.t1 range=chrLG1:1047971-1161345 5'pad=0 3'pad=0 strand=+ repeatMasking=none to this : >oreNil2_augustusGene_g25.t1 Basically removing all the lines after the space. I know we can do this wi ...
fasta header sed awk written 3.8 years ago by wanziyi8950 • updated 3.8 years ago by kapil.joshi03680
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Comment: C: How to extract coordinates of first exons from .gtf file.
... Thank you! HTseq seems promising and I think I found some leads in the TSS Plot. ...
written 4.3 years ago by wanziyi8950
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How to extract coordinates of first exons from .gtf file.
... Hi All,    Supposed I have a .gtf file with the exons of all genes in a given genome. I would like to extract the first exon coordinate of each gene from the .gtf file. How should I get started?   regards,   Ziyi ...
gtf genome exon rna-seq written 4.3 years ago by wanziyi8950 • updated 4.3 years ago by geek_y10k
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From FASTA file to GO-annotation
... Dear All, I have found a total list of about 3000 transcripts that I am interested in their gene ontology functions. I have the .fasta file of each transcripts. Can anyone advise on how should I go about to extract the GO symbols for each genes? The pipeline I can think of is input the .fasta file ...
rna-seq go written 4.4 years ago by wanziyi8950 • updated 4.4 years ago by SES8.3k
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<Data Munging> Convert Methylation Percentage to Number of Reads
... Dear all, I have a file as shown below: chrBase chr base strand coverage freqC freqT chrLG1.6955 chrLG1 6955 R 12 0.00 100.00     I would like to print this as a new file with the following format : Chr"/t"Position"/t"Coverage"/t"Numbers_ ...
methylation conversion written 4.5 years ago by wanziyi8950 • updated 4.5 years ago by Devon Ryan94k
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BEDgraph to BED/bam
... Hi guys,   Any tools or software available for converting bedgraph to bed and then to bam? I would like to extract CpG methylation calls using bismark and then save them in Bam format then convert them to bam using bedtools. I saw some references to manually convert bedgraph to bed via UNIX comm ...
bed written 4.6 years ago by wanziyi8950
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Comment: C: Combining all biological replicates
... Isolates as in 3 strains of different bacteria/virus ? ...
written 4.7 years ago by wanziyi8950
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Comment: A: Help : How To Connect To Genome-Mysql.Cse.Ucsc.Edu.
... Hi all, I tried the following command: $ mysql --user=genome --host=genome-mysql.cse.ucsc.edu What I got was this: ERROR 2003 (HY000): Can't connect to MySQL server on 'genome-mysql.cse.ucsc.edu' (110) Any idea what is wrong here?   Thanks in advance.   ...
written 4.7 years ago by wanziyi8950
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Comment: A: Help : How To Connect To Genome-Mysql.Cse.Ucsc.Edu.
... Hi all, I tried the following command: $ mysql --user=genome --host=genome-mysql.cse.ucsc.edu What I got was this: ERROR 2003 (HY000): Can't connect to MySQL server on 'genome-mysql.cse.ucsc.edu' (110) Any idea what is wrong here?   Thanks in advance.   ...
written 4.7 years ago by wanziyi8950

Latest awards to wanziyi89

Voter 17 months ago, voted more than 100 times.
Popular Question 2.5 years ago, created a question with more than 1,000 views. For From FASTA file to GO-annotation
Popular Question 2.9 years ago, created a question with more than 1,000 views. For From FASTA file to GO-annotation
Popular Question 2.9 years ago, created a question with more than 1,000 views. For How to extract coordinates of first exons from .gtf file.
Popular Question 2.9 years ago, created a question with more than 1,000 views. For From FASTA file to GO-annotation
Popular Question 3.3 years ago, created a question with more than 1,000 views. For From FASTA file to GO-annotation
Student 4.4 years ago, asked a question with at least 3 up-votes. For From FASTA file to GO-annotation
Supporter 4.5 years ago, voted at least 25 times.

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