User: Sheldon

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Sheldon4.0k
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Posts by Sheldon

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Answer: A: Where to download refseq gene data
... Download Human and Mouse refGene from UCSC with bash wget wget -c -O mm9.refGene.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/mm9/database/refGene.txt.gz wget -c -O mm10.refGene.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/refGene.txt.gz wget -c -O hg19.refGene. ...
written 7 days ago by Sheldon4.0k
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Comment: C: Where to download refseq gene data
... Any SQL or Perl script to do it? ...
written 8 days ago by Sheldon4.0k
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Comment: C: Method to Check Fastq Completeness after Fastq-dump
... By the way: how to deal with Resume Broken Download Problem for fastq-dump ? ...
written 8 days ago by Sheldon4.0k
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Answer: A: How can I find SRA MD5 checksums for FASQ files?
... Try this one. When you didn't remove SRA files, you can use the following: for i in `ls *.gz`; do SRR=${i%%_*}; echo $SRR >> list.txt; done for j in `sort -u list.txt` do vdb-validate $j done if you have already removed SRA and only ...
written 8 days ago by Sheldon4.0k
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Comment: C: Method to Check Fastq Completeness after Fastq-dump
... Thanks. The method you mention works in some way. However, for the majority situation, it doesn't work. for example: fastq-dump --split-files --gzip SRR949203 if you just download the SRA files, I think it is okay to use vdb-validate SRR949203 ...
written 8 days ago by Sheldon4.0k
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Method to Check Fastq Completeness after Fastq-dump
... Hi All, What's your method to check the completeness of the fastq file after the download by fastq-dump from SRA database? I always find some non-completeness fastqs after the fastq-dump. Thanks. ...
fastq-dump completeness written 8 days ago by Sheldon4.0k
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Implemention of Maximum-likelihood estimation for true-indels in CRISPR-Cas9
... Hi All, I find the Maximum-likelihood estimation for true-indels in CRISPR-Cas9 was quite popular, however, I didn't find its authoritative version in the github (R version)? Refrence: Protocol: Genome-scale CRISPR-Cas9 Knockout and Transcriptional Activation Screening, 2016, Biorxiv. DNA tar ...
mle crispr-cas9 written 9 days ago by Sheldon4.0k
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How to match the sample type for serial of SRX ID
... Hi All, Suppose I have hundreds of SRX ID, such as SRX209456, I want to search what kinds of tissue, or other sample information, they are. Is there any script or command or SQL to do that? Thanks. ...
sql srx written 10 days ago by Sheldon4.0k
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Forum: Segmentation method comparisons: HMM, CBS, RS
... Hi All, Segmentation processing is quite important in CNV and DMR analysis. However, is there any paper to compare the power for the difference methods? How many Segmentation method could be applied? I only know HMM, CBS, Rank Segmentation, is there any other popular methods? Regards, ...
rank hmm forum cbs segmentation written 13 days ago by Sheldon4.0k • updated 2 days ago by Aerval200
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Comment: C: T Cell Specific Gene Expression Data
... Hey, Alexis, Please share the human data. I am sure it would be widely cited. Thanks. ...
written 13 days ago by Sheldon4.0k

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