User: yuabrahamliu
yuabrahamliu • 40
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- 5 months ago
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- 1 year, 9 months ago
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Posts by yuabrahamliu
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... I see. Thank you for the help! ...
written 5 months ago by
yuabrahamliu • 40
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... Hello everyone,
Maybe my questions are really easy to some experts, but as a new to TCGA data, I indeed feel confused. So if anyone could give me any ideas, I will be appreciated.
I want to do some analysis on the TCGA level-3 DNA methylation data from various cancer types. However, my question is ...
written 5 months ago by
yuabrahamliu • 40
0
votes
1
answer
478
views
1
answer
... Hello everyone,
Maybe my questions are really easy to some experts, but as a new to TCGA data, I indeed feel confused. So if anyone could give me any ideas, I will be appreciated.
I want to do some analysis on the TCGA level-3 DNA methylation data from various cancer types. However, my question is ...
written 5 months ago by
yuabrahamliu • 40
• updated
5 months ago by
Charles Warden ♦ 7.0k
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... **Description**
Dr. Lana Garmire's translational bioinformatics group in the Department of Computational Medicine and Bioinformatics at University of Michigan has multiple postdoc positions for highly competent and motivated researchers immediately. Current projects include (1) Single-cell genomics ...
written 8 months ago by
yuabrahamliu • 40
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... Thank you so much for reply. Because I wanted to extract reads on some whole chromosomes, and just use their name to select the whole without the start and end coordinates in the bed file, I used xargs instead of the -L flag of samtools. I have found the issue is that the header of the bam file make ...
written 11 months ago by
yuabrahamliu • 40
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... Hi, I have a bam file. Then, to extract specific regions of that file, I used the command
cat chrs.txt | xargs -n 1 samtools view -@ 10 -b -h bd.bam > bd2.bam
where `chrs.txt` is the file containing the regions to be exacted, like
> chr1
>
> chr1_random
>
> chr2
Then, after ...
written 11 months ago by
yuabrahamliu • 40
• updated
11 months ago by
swbarnes2 ♦ 6.0k
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Comment:
C: Trim Paired-end Fastq Files
... Awesome. I think it is a very useful tool, fastq-pair. ...
written 12 months ago by
yuabrahamliu • 40
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Comment:
C: Trim Paired-end Fastq Files
... Thank you. I used wc -l to check the total line, and then divide them by 4. ...
written 12 months ago by
yuabrahamliu • 40
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6 follow
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... Hi all,
Maybe I'm asking a too basic question, but I really feel confused. I have R1.fastq file and R2.fastq file from the paired-end RNA-seq. As far as I know, the read order in R1 and R2 files should be the same, namely the reads in the same pair should get the same rank in R1 and R2 respectively ...
written 12 months ago by
yuabrahamliu • 40
• updated
12 months ago by
h.mon ♦ 26k
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... I know some databases containing a great source of protein binding information, such as STRING and BIOGRID. But I found although these databases record the protein binding pairs, they don't have much information on the binding domain mediating the their binding, which might be useful when analyzing ...
written 13 months ago by
yuabrahamliu • 40
• updated
12 months ago by
Biostar ♦♦ 20
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11 months ago,
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For BigWig file of strand-specific RNA-seq data
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