User: yuabrahamliu

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yuabrahamliu40
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5 months ago
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Posts by yuabrahamliu

<prev • 27 results • page 1 of 3 • next >
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Comment: C: TCGA DNA methylation data pipeline
... I see. Thank you for the help! ...
written 5 months ago by yuabrahamliu40
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TCGA methylation data normalization
... 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 ...
normalization tcga methylation data written 5 months ago by yuabrahamliu40
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TCGA DNA methylation data pipeline
... 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 ...
dna methylation tcga pipeline written 5 months ago by yuabrahamliu40 • updated 5 months ago by Charles Warden7.0k
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Job: Bioinformatic Postdoc Position at University of Michigan
... **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 ...
postdoc bioinformatic job written 8 months ago by yuabrahamliu40
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Comment: C: samtools sort: truncated file. Aborting
... 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 yuabrahamliu40
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samtools sort: truncated file. Aborting
... 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 ...
truncated file samtools written 11 months ago by yuabrahamliu40 • updated 11 months ago by swbarnes26.0k
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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 yuabrahamliu40
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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 yuabrahamliu40
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Trim Paired-end Fastq Files
... 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 ...
trimmomatic paired-end rna-seq written 12 months ago by yuabrahamliu40 • updated 12 months ago by h.mon26k
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Protein binding domain database
... 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 ...
database protein binding domain written 13 months ago by yuabrahamliu40 • updated 12 months ago by Biostar ♦♦ 20

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Popular Question 11 months ago, created a question with more than 1,000 views. For BigWig file of strand-specific RNA-seq data

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