User: yuabrahamliu

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yuabrahamliu10
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Posts by yuabrahamliu

<prev • 13 results • page 1 of 2 • next >
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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 15 days ago by yuabrahamliu10
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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 16 days ago by yuabrahamliu10
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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 16 days ago by yuabrahamliu10 • updated 16 days ago by Devon Ryan76k
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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 23 days ago by yuabrahamliu10 • updated 23 days ago by swbarnes23.1k
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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 23 days ago by yuabrahamliu10 • updated 15 days ago by Biostar ♦♦ 20
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Comment: C: calculate RPKM from featureCounts result
... I see. Thank you so much! ...
written 11 weeks ago by yuabrahamliu10
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calculate RPKM from featureCounts result
... Hi all, I have a question. I got the read counts result from some microRNA-seq bam files by featureCounts. Then, I want to transform the counts to RPKM. I think maybe the rpkm() function of edgeR is helpful. However, my question is whether I need to normalize the counts result before using the rpkm( ...
rna-seq written 11 weeks ago by yuabrahamliu10 • updated 11 weeks ago by cindy.perscheid90
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Comment: A: Speed up Tophat2 running
... It really took about 6 hours to complete the first sample. Thank you. ...
written 3 months ago by yuabrahamliu10
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Speed up Tophat2 running
... Hi, all. I'm starting to use tophat2 to map dUTP strand-specific, paired-end RNA-seq data to mm9 genome. Each sample pair includes 2 samples about 500M large. However, I find that the run time is a bit too long. My commandline is like this: `tophat2 -o tophatoutput -p 28 --no-coverage-search --libr ...
dutp tophat2 rna-seq written 3 months ago by yuabrahamliu10
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Comment: C: BigWig file of strand-specific RNA-seq data
... Thank you so much for your help. I have changed `genomeCoverageBed` to `bamCoverage`, but unfortunately, the plus and minus strands still cannot be distinguished. I feel really confused, I don't know if there is something wrong with my code. Do you have any suggestions on dUTP data? Thank you. ``` ...
written 3 months ago by yuabrahamliu10

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