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User: yuabrahamliu

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yuabrahamliu • 30
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Posts by yuabrahamliu

<prev • 18 results • page 1 of 2 • next >
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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 10 days ago by yuabrahamliu • 30
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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 5 weeks ago by yuabrahamliu • 30 • updated 5 weeks ago by swbarnes2 ♦ 3.6k
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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 10 weeks ago by yuabrahamliu • 30 • updated 20 days 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 12 weeks ago by yuabrahamliu • 30
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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 3 months ago by yuabrahamliu • 30 • updated 3 months ago by genecats.ucsc • 500
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Comment: C: k-mer enrichment analysis
... That's a good idea. But the problem is that I have the exact gene name list of the mRNAs able to bind the protein, but don 't have fastq files. So I want to do the kmer analysis on the FASTA sequence of the binding fragments of the mRNAs. I have checked khmer, but it seems it only works on sequencin ...
written 4 months ago by yuabrahamliu • 30
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Comment: C: k-mer enrichment analysis
... An RNA binding protein can bind to the experimental group while not to the control group. So want to see if any k-mer sequence is enriched in the experimental group. Maybe it is a kind of bind motif of the protein. ...
written 4 months ago by yuabrahamliu • 30
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k-mer enrichment analysis
... Hi all, I have 2 groups of RNAs, one is the experimental group, the other is the control group. What I need to do is to check if there is some k-mer sequences highly enriched in the experimental group compared to the control group, or vice versa. My question is that, 1) How can I get the RNA sequ ...
rna-seq written 4 months ago by yuabrahamliu • 30 • updated 4 months ago by Devon Ryan ♦ 80k
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featureCounts generates low assigned rate
... Hi all, I'm processing 2 RNA-seq data. One has a fragment insertion size less than 30 bp, the other less than 500 bp. The mapping result from STAR is good, both of them have more than 95% reads with a MAPQ value > 10. However, what made me confuse is that, when I used featureCounts to count the ...
rna-seq written 4 months ago by yuabrahamliu • 30 • updated 4 months ago by swbarnes2 ♦ 3.6k
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pre-miRNA annotation and quantification
... Hi all, I have a question about pre-miRNA, because I need to quantify pre-miRNA expression level. I think the first thing I need to do is to make clear of the pre-miRNA annotation and their coordinates, but I really don't know how to get these information. Is there any GTF files on pre-miRNA, or an ...
rna-seq written 4 months ago by yuabrahamliu • 30 • updated 4 months ago by Biostar ♦♦ 20

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