User: wm

gravatar for wm
wm490
Reputation:
490
Status:
Trusted
Location:
China
Last seen:
6 days, 21 hours ago
Joined:
8 years, 10 months ago
Email:
w*******@gmail.com

Posts by wm

<prev • 87 results • page 1 of 9 • next >
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Comment: C: STAR genomeLoad issue
... There is probably a typo in your script. (you could paste your script here: line16 to line18) like, your command is in multiple lines, but missing `\` at the end of `line-16`. ...
written 3 months ago by wm490
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Comment: C: Bowtie2 error :: (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
... Fine, the details what you did help other to reproduce your problem. I guess, one possible reason, the sra file is truncated that downloaded by `fastq-dump` (not tested), Anyway, it is **recommended** to download files using `prefetch`, not `fastq-dump`. if you tried as exactly as ...
written 4 months ago by wm490
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Comment: C: Bowtie2 error :: (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
... Would you paste the command here? and also one of the SRR number. If it is paired end reads, use `--split-3` will save each read into separate files. (Read 1, read 2, and orphaned reads(if exists) ). but --split-files will not. So, try `--split-3` if you can make sure the SRA contains Pair ...
written 4 months ago by wm490
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Comment: C: STAR genomeLoad issue
... Thanks so much. it works. after a few test, I found, if the script was interrupted for some reason. the loaded genome would still saved in memory. Even in this situation after several runs, I could clear the memory to fix it (with `root`). Anyway, I could run the `function` in parallel now, ...
written 4 months ago by wm490
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Comment: C: featureCounts: Low % assigned fragments and discrepancy between STAR alignment m
... 1. Yes, `infer_experiment.py` is a easy-to-run program, to check out the library. 2. As you mentioned, you get 65% properly assigned reads with (`-s 1`) and 10% with (`-s 2`). so, there are >20% reads could not map to the `features` from the `gtf` file, it is deserved a closer check of you ...
written 4 months ago by wm490
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Comment: C: STAR genomeLoad issue
... Hi Ryan, does it possible to check whether the genome is loaded in the memory or not, and how? I wrap the `STAR` command in a function. if it is possible to check the `genome` in memory, I can choose which `--genomeLoad` option to use, and the genome can be removed after all functions finished. ...
written 5 months ago by wm490
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Comment: C: How to filter unique reads from sam file?
... it turns out that tag `YT:Z:CP` report reads "exact 1 time" and reads with "concordantly > 1 times" once. How can I filter the 'exact 1 time` reads only? ...
written 5 months ago by wm490
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Answer: A: GGplot2 coord flip problem
... We can use the `str_wrap( )` function from `stringr` package to process the text, here is a example on `scale_x_discrete()`. we can also apply this function to other text content. # R code library(ggplot2) # version 3.3.0 library(stringr) # version 1.4.0 library(patchwork) # versio ...
written 5 months ago by wm490
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Comment: C: Drosophila reference genomes
... here is the reference data for fruitfly on UCSC, And I used to batch download genomes from UCSC, there is `rsync` service, easy to maintain the local dataset. see here: http://hgdownload.soe.ucsc.edu/downloads.html#fruitfly $ rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/dm6/bigZip ...
written 5 months ago by wm490
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Comment: C: Drosophila reference genomes
... We mostly use the reference from UCSC (dm6, BDGP6), and annotations from flybase: http://flybase.org ...
written 5 months ago by wm490

Latest awards to wm

Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Extract data from a large bed file
Popular Question 4 months ago, created a question with more than 1,000 views. For How Can Soap2Sam.Pl Be More Fast?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Extract data from a large bed file
Scholar 5 months ago, created an answer that has been accepted. For A: Extract data from a large bed file
Scholar 6 months ago, created an answer that has been accepted. For A: Extract data from a large bed file
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Pheatmap Annotation
Popular Question 16 months ago, created a question with more than 1,000 views. For How Can Soap2Sam.Pl Be More Fast?
Great Question 2.9 years ago, created a question with more than 5,000 views. For Error When Install Samtools, Version `Zlib_1.2.3.3` Not Found
Good Answer 3.6 years ago, created an answer that was upvoted at least 5 times. For A: Pheatmap Annotation
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Popular Question 6.5 years ago, created a question with more than 1,000 views. For Error When Install Samtools, Version `Zlib_1.2.3.3` Not Found

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