User: yuabrahamliu

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yuabrahamliu30
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Posts by yuabrahamliu

<prev • 23 results • page 1 of 3 • next >
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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 9 weeks ago by yuabrahamliu30
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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 9 weeks ago by yuabrahamliu30 • updated 9 weeks ago by swbarnes24.0k
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Comment: C: Trim Paired-end Fastq Files
... Awesome. I think it is a very useful tool, fastq-pair. ...
written 9 weeks ago by yuabrahamliu30
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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 9 weeks ago by yuabrahamliu30
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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 9 weeks ago by yuabrahamliu30 • updated 9 weeks ago by h.mon19k
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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 3 months ago by yuabrahamliu30 • updated 3 months ago by Biostar ♦♦ 20
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Screen reads with specific sub-sequences from BAM file
... Hi all, Could anyone give me some help? I have an RNA-seq bam file. What I want to do is to select the reads in it that have additional continuous A strings at the 3'end of the reads. (i.e. these reads can be divided into 2 parts, the 5'end part can be aligned to the genome well, but the 3'end c ...
screen bam reads sequence rna-seq written 4 months ago by yuabrahamliu30 • updated 4 months ago by swbarnes24.0k
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GRO-seq transcription rate
... Hi all, I'm working on a set of GRO-seq data to calculate gene transcription rate. DRB was used during the experiment to release Pol2 and made a part of the original read band covering the genes at 0 min have some "blank". Then the transcription rate would be calculated by dividing the "blank" leng ...
gro-seq grohmm hmm drb-seq transcription rate written 5 months ago by yuabrahamliu30 • updated 3 months ago by Biostar ♦♦ 20
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strand-specific metagene analysis
... Hi all, I want to ask for some help on strand-specific RNA-seq metagene construction. I have aligned some adapter-based strand-specific RNA-seq to mm10 genome using STAR and then I want to construct a metagene plot on some group of genes using HTSeq, but I found that for many specfic gene region, b ...
htseq strand-specific rna-seq metagene written 6 months ago by yuabrahamliu30
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Question on UCSC genome browser display
... Hi all, I have a question on USCS genome browser display. After I uploaded my custom track to the genome browser. Many times I need to zoom in the figure to see some details. It can always be done via Shift + drag-and-click manipulation. My question is how can I reset the browser to zoom in directl ...
ucsc genome browser written 6 months ago by yuabrahamliu30 • updated 6 months ago by genecats.ucsc560

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