User: MatthewP

gravatar for MatthewP
MatthewP780
Reputation:
780
Status:
Trusted
Location:
China
Last seen:
4 hours ago
Joined:
2 years, 5 months ago
Email:
m***********@gmail.com

Posts by MatthewP

<prev • 194 results • page 1 of 20 • next >
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Comment: C: Customize fold change legend values in ComplexHeatmap
... It's `col = circlize::colorRamp2(c(-2,0,2), c("blue", "white", "red"))` not `col_fun`. Use `?Heatmap` to check parameters correct name. ...
written 5 days ago by MatthewP780
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Comment: C: Access metadata in GEO expression datasets
... The error message is telling you don't have enough device space. ...
written 7 days ago by MatthewP780
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Comment: C: Help with Rstudio in Anaconda Navigator
... Maybe install R packages from rstudio won't have such problem. ...
written 11 days ago by MatthewP780
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Comment: C: key lookup changes with AnnotationDbi version
... And what's your result compare of `keys`? For example `setdiff(computer1_keys, computer2_keys)` ...
written 11 days ago by MatthewP780
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Comment: C: DESeq2 Shrink cutoff
... I always use shrinked result. Shrinkage only change foldchange not p value. Mean counts value is easier affected by outlier value. ...
written 11 days ago by MatthewP780
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Comment: C: key lookup changes with AnnotationDbi version
... Try `packageVersion("hgu219.db")` to check exact version of "hgu219.db", don't guess. ...
written 11 days ago by MatthewP780
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ATAC-seq many reads first base is "N"
... I have fastq file of ATAC-seq but many reads start with one "N" base, I wonder what could be the reason. Reads example: @A00838:273:HCV7KDSXY:4:1101:1506:1000 1:N:0:AGGCAGAA+TATCCTCT NATCCAGAAAAAAAAAAAATCATGACCAAGCTTACCGTCCCCACTTAAAT + #FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF ...
atac-seq written 28 days ago by MatthewP780
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Answer: A: paired reads aligned at the same genomic position
... Paired reads align at same position probably because some insert fragments is too short that even shorter than your reads, you can use `fastp` to get fragment length distribution report, so you can see is there some fragments too short. I don't think you need to remove one of them, you can see [b ...
written 29 days ago by MatthewP780
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Comment: A: Bowtie2 alignment help for ATAC-seq
... [This guideline](https://informatics.fas.harvard.edu/atac-seq-guidelines.html) also add `-k 10` but gives no reason. I guess this may relative to some very short fragments? ...
written 4 weeks ago by MatthewP780
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Comment: C: HISAT2- (ERR): hisat2-align exited with value 134
... Can you post first record(4 lines) of your fastq file? ...
written 4 weeks ago by MatthewP780

Latest awards to MatthewP

Popular Question 16 days ago, created a question with more than 1,000 views. For How to apply GATK on mtDNA sequencing data?
Scholar 4 weeks ago, created an answer that has been accepted. For A: How to convert data from NCBI E-utilities.efetch to python data object?
Popular Question 5 weeks ago, created a question with more than 1,000 views. For How to apply GATK on mtDNA sequencing data?
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Some questions about call variants for mtDNA using GATK HaplotypeCaller
Popular Question 3 months ago, created a question with more than 1,000 views. For Some questions about call variants for mtDNA using GATK HaplotypeCaller
Scholar 3 months ago, created an answer that has been accepted. For A: How to convert data from NCBI E-utilities.efetch to python data object?
Scholar 4 months ago, created an answer that has been accepted. For A: How to convert data from NCBI E-utilities.efetch to python data object?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Problem with downloading GSE file by GEOquery
Popular Question 4 months ago, created a question with more than 1,000 views. For How to process (seems) Agilent microarrry data?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Problem with downloading GSE file by GEOquery
Scholar 5 months ago, created an answer that has been accepted. For A: How to convert data from NCBI E-utilities.efetch to python data object?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Problem with downloading GSE file by GEOquery
Popular Question 6 months ago, created a question with more than 1,000 views. For Some questions about call variants for mtDNA using GATK HaplotypeCaller
Popular Question 7 months ago, created a question with more than 1,000 views. For How to use snpSift annotate -info option to annotate specific fields of INFO
Popular Question 7 months ago, created a question with more than 1,000 views. For How to use snpSift annotate -info option to annotate specific fields of INFO
Popular Question 8 months ago, created a question with more than 1,000 views. For Some questions about write human mitochondrial variants into VCF file
Scholar 10 months ago, created an answer that has been accepted. For A: How to convert data from NCBI E-utilities.efetch to python data object?
Scholar 10 months ago, created an answer that has been accepted. For A: How to convert data from NCBI E-utilities.efetch to python data object?
Scholar 11 months ago, created an answer that has been accepted. For A: How to convert data from NCBI E-utilities.efetch to python data object?
Centurion 12 months ago, created 100 posts.
Scholar 14 months ago, created an answer that has been accepted. For A: How to convert data from NCBI E-utilities.efetch to python data object?
Appreciated 15 months ago, created a post with more than 5 votes. For A: Problem with downloading GSE file by GEOquery
Scholar 15 months ago, created an answer that has been accepted. For A: How to convert data from NCBI E-utilities.efetch to python data object?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Problem with downloading GSE file by GEOquery
Scholar 21 months ago, created an answer that has been accepted. For A: How to convert data from NCBI E-utilities.efetch to python data object?

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