User: yuabrahamliu

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yuabrahamliu10
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Posts by yuabrahamliu

<prev • 6 results • page 1 of 1 • next >
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Comment: A: Speed up Tophat2 running
... It really took about 6 hours to complete the first sample. Thank you. ...
written 6 days 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 7 days 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 8 days ago by yuabrahamliu10
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BigWig file of strand-specific RNA-seq data
... Hi all, I began to process strand-specific RNA-seq data from dUTR method library these days. I added the flag `--rna-strandness RF` to the default `hisat2` commandline on paired-end RNA-seq data and each line of the final bam file also got a `XS:A:+` or `XS:A:-` value to indicate the plus or minus s ...
dutp bigwig strand-specific rna-seq written 9 days ago by yuabrahamliu10 • updated 9 days ago by Devon Ryan73k
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coordinate of BAM and BED
... Hi all, I want to use `bedtools multicov` to count the RNAseq reads in specific bed file intervals (containing all the intron intervals of mm10 genome downloaded from UCSC). However, I noted that the BED file coordinate is 0-based, while the BAM file used by `bedtools multicov` was sorted by samtool ...
genome alignment rna-seq written 14 days ago by yuabrahamliu10 • updated 14 days ago by Devon Ryan73k
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Questions on Conda Installation on Linux Subsystem for Windows
... Hi all, I have installed the Ubuntu subsystem on Windows 10 (Ubuntu version 16.04). Then, I run the command curl http://data.biostarhandbook.com/install/aptget.txt | xargs sudo apt-get -y install (follow the command line on the Biostar Handbook) on the subsystem to install libraries. All the ...
software error written 5 weeks ago by yuabrahamliu10 • updated 15 hours ago by Biostar ♦♦ 20

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