User: Julie Zhu

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Julie Zhu4.1k
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Lihua Julie Zhu, Ph.D

Professor

Department of Molecular, Cell and Cancer Biology (MCCB)

Head of MCCB Bioinformatics Core

Program in Bioinformatics and Integrative Biology

Program in Molecular Medicine

University of Massachusetts Medical School

364 Plantation Street, Room 613

Worcester, MA 01605

508-856-5256 phone

(508) 856 5460 fax

https://profiles.umassmed.edu/display/129880

Posts by Julie Zhu

<prev • 617 results • page 1 of 62 • next >
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Comment: C: QuasR::qAlign: how to specify maximum allowed number of mismatches and output al
... Hi Michael, Thank you very much for the detailed information! It’s very helpful! Best regards, Julie ...
written 4 weeks ago by Julie Zhu4.1k
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Answer: A: GUIDEseq Error using offTargetAnalysisOfPeakRegions
... Hi Tom, The 5th column stores score, which should be numeric. Therefore, it should only contain numbers. FYI, I have modified the script which is able to handle peak bed files with 3 or more columns. Please download the updated version GUIDEseq 1.7.1 using git clone git@git.bioconductor.org:pac ...
written 5 weeks ago by Julie Zhu4.1k
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Answer: A: GUIDEseq Error using offTargetAnalysisOfPeakRegions
... Hi Tom, Please add strand information to the peak bed file that should resolve the issue. offTargetAnalysisOfPeakRegions was internally called by GUIDEseqAnalysis which generates strand information automatically. You made me realize that the function offTargetAnalysisOfPeakRegions could be very u ...
written 5 weeks ago by Julie Zhu4.1k
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Answer: A: GUIDEseq Error using offTargetAnalysisOfPeakRegions
... Hi Tom, I tried to run the analysis with a smaller input bed file, and did not get the same error. I am wondering whether the error is from running the analysis with the entire dataset or just chr6 you shared with me. Thanks! Best, Julie ...
written 5 weeks ago by Julie Zhu4.1k
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Answer: A: GUIDEseq Error using offTargetAnalysisOfPeakRegions
... Hi Tom, I tried to run the analysis with a smaller input bed file, and did not get the same error. I am wondering whether the error is from running the analysis with the entire dataset or just chr6 you shared with me. Thanks! Best, Julie ...
written 5 weeks ago by Julie Zhu4.1k
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Answer: A: GUIDEseq BED input error
... Hi Tom, Please set peaks and gRNAs to the file path of your bed file and gRNAs fasta file respectively. library("BSgenome.Hsapiens.UCSC.hg38") library(TxDb.Hsapiens.UCSC.hg38.knownGene) library(org.Hs.eg.db) peaks <- "i505i706.sort.bed" gRNAs <- "SpyDTS4.fa" outputDir = getwd() offTarg ...
written 5 weeks ago by Julie Zhu4.1k
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QuasR::qAlign: how to specify maximum allowed number of mismatches and output all alignments
... Dear QuasR developers, I would like to use the qAlign function in QuasR. However, I do not see any parameters for specifying the number of mismatches allowed (-v parameter in bowtie) or the number of alignments (-k parameter in bowtie) to output for a multi-mapping read. According to the help menu, ...
quasr written 6 weeks ago by Julie Zhu4.1k • updated 4 weeks ago by Michael Stadler330
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Comment: C: CRISPRseek help to generate gRNAs for CRISPRi library
... Hi Kathleen, Here are the scripts offTargetSearchBatch.R and offTargetSearchBatch.bsub, which I used for batch analysis in high-performance computing environment. After modifying the parameters to fit your own needs, you can run the script in the cluster by typing the following command. ./offTarg ...
written 6 weeks ago by Julie Zhu4.1k
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Comment: C: CRISPRseek help to generate gRNAs for CRISPRi library
... You are welcome, Katherine! I suggest to set n.cores = 6 to test whether it works as expected. If you have a file with lots of gRNAs to search for offTargets, it will be more effective to run several searches each with a subset of the gRNAs. Best regards, Julie ...
written 6 weeks ago by Julie Zhu4.1k
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Answer: A: CRISPRseek help to generate gRNAs for CRISPRi library
... Hi Katherine, I suggest set exportAllgRNAs = "fasta" and annotatePaired = FALSE in addition to the parameters you set, such as findPairedgRNAOnly = FALSE, findgRNAsWithREcutOnly = FALSE, enable.multicore=TRUE, n.cores.max=60, annotateExon = FALSE, If you are not interested in identifying offTa ...
written 7 weeks ago by Julie Zhu4.1k

Latest awards to Julie Zhu

Popular Question 12 months ago, created a question with more than 1,000 views. For CRISPRseek question on scoring
Popular Question 12 months ago, created a question with more than 1,000 views. For GEOquery
Popular Question 12 months ago, created a question with more than 1,000 views. For CRISPRseek question on scoring
Scholar 12 months ago, created an answer that has been accepted. For A: createBarcodeFasta in GUIDEseq
Popular Question 12 months ago, created a question with more than 1,000 views. For Biostrings::matchPattern,extract sequences
Popular Question 16 months ago, created a question with more than 1,000 views. For org.Sc.sgd.db: Yeast ensembl ID to entrez ID conversion problem
Popular Question 20 months ago, created a question with more than 1,000 views. For Biostrings::matchPattern,extract sequences
Popular Question 20 months ago, created a question with more than 1,000 views. For GEOquery
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Biostrings::matchPattern,extract sequences
Popular Question 2.6 years ago, created a question with more than 1,000 views. For GEOquery
Popular Question 2.6 years ago, created a question with more than 1,000 views. For CRISPRseek question on scoring
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: What are out-of-bound ranges? Is it necessary to get rid of them?
Scholar 2.6 years ago, created an answer that has been accepted. For A: How to find nearest CpG islands around miRNA genes using granges?
Scholar 2.6 years ago, created an answer that has been accepted. For A: GUIDESeq analysis - handling biological and technical replicates
Scholar 2.6 years ago, created an answer that has been accepted. For A: offTargetAnalysis() Error in weights %*% mismatch.pos : non-conformable argument
Scholar 2.6 years ago, created an answer that has been accepted. For A: DistanceToNearest Not giving nearest Range
Scholar 2.6 years ago, created an answer that has been accepted. For A: What are out-of-bound ranges? Is it necessary to get rid of them?
Scholar 2.6 years ago, created an answer that has been accepted. For A: createBarcodeFasta in GUIDEseq
Popular Question 2.8 years ago, created a question with more than 1,000 views. For build TSS from biomaRt for ChIPpeakAnno, how to decide the mm9 and mm10 assembly?
Scholar 5.1 years ago, created an answer that has been accepted. For A: ChIPpeakAnno: Non-empty IRange object in case of no overlap
Autobiographer 5.3 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 5.3 years ago, created 100 posts.

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