User: MatthewP

gravatar for MatthewP
MatthewP880
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880
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Trusted
Location:
China
Last seen:
4 hours ago
Joined:
2 years, 9 months ago
Email:
m***********@gmail.com

Posts by MatthewP

<prev • 223 results • page 1 of 23 • next >
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Comment: C: About shell script
... You said `sh A.txt` failed, can you post error message? ...
written 20 days ago by MatthewP880
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Answer: A: Get top-contribution variant name for PCA result
... Add line and arrows from (0, 0) to `pca$rotation` on your PCA biplot. Ther higher absolute values in `pca$rotation` matrix means higher contribution. So longer line and arrows means higher contribution. > head(mtcars) ...
written 20 days ago by MatthewP880
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Answer: A: question about R language 'for' loop
... Use `ggsave` function to save ggplot picture. ...
written 26 days ago by MatthewP880
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Comment: C: Bowtie2 command does not produce output file
... Hello, you said no output file. Does your run get any error? Can you post some running log? The reference of bowtie2, can you check the name? For example my bowtie2 index file is "GRCh38.1.bt2, GRCh38.2.bt2, GRCh38.3.bt2..." so my `-x` is `-x GRCh38` that remove file extention from file name. Your ` ...
written 4 weeks ago by MatthewP880
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Answer: A: How to create interval list from reference fasta or dict file?
... Ok I can answer myself. # Create dict and faidx index for fasta gatk CreateSequenceDictionary -R GRCh38.primary_assembly.genome.fa samtools faidx GRCh38.primary_assembly.genome.fa # get fasta bed file awk -v FS="\t" -v OFS="\t" '{print $1 FS "0" FS $2}' GRCh38.primary_assembly.g ...
written 4 weeks ago by MatthewP880
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Comment: C: How to create interval list from reference fasta or dict file?
... Ok, this won't work, parse dict file to `-L` parameter of gatk command `HaplotypeCaller` will cause error. ...
written 4 weeks ago by MatthewP880
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Comment: C: How to create interval list from reference fasta or dict file?
... Ok, I already created this dict file, but don't know this can serve as interval list, thanks. ...
written 4 weeks ago by MatthewP880
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How to create interval list from reference fasta or dict file?
... I am using GATK pipeline on WGS data. My BAM files is aligned to GRCh38 from GENCODE. So I want to create interval file for this GRCh38 instead of download from GATKbundle, because some of their contigs have different names. For example "KI270706.1" in GENCODE's GRCh38 is "chr1_KI270706v1_random" in ...
gatk written 4 weeks ago by MatthewP880
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Comment: C: How to get gene level of differential expression from 2 color channel array with
... Yes I know dye effect = dye bias. Just this dataset condition "sensitive" has too little number of probes that expression differentially and "DyeEffect" has too many, makes me confusing. ...
written 5 weeks ago by MatthewP880
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Comment: C: How to get gene level of differential expression from 2 color channel array with
... Hello Gordon Smyth. Do you know how to detect dye bias? I added dye effect in design model. > desigN Sensitive DyeEffect GSM4518466 1 1 GSM4518467 -1 1 GSM4518468 1 1 GSM4518469 -1 1 GSM4518470 ...
written 5 weeks ago by MatthewP880

Latest awards to MatthewP

Popular Question 24 days ago, created a question with more than 1,000 views. For How to show selected node lables only in cytoscape?
Scholar 26 days 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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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?
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Very large fastq files from RNA-seq
Popular Question 3 months ago, created a question with more than 1,000 views. For How to show selected node lables only in cytoscape?
Popular Question 3 months ago, created a question with more than 1,000 views. For How to show selected node lables only in cytoscape?
Popular Question 4 months ago, created a question with more than 1,000 views. For How to apply GATK on mtDNA sequencing data?
Popular Question 4 months ago, created a question with more than 1,000 views. For How to apply GATK on mtDNA sequencing data?
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?
Popular Question 5 months ago, created a question with more than 1,000 views. For How to apply GATK on mtDNA sequencing data?
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 Some questions about call variants for mtDNA using GATK HaplotypeCaller
Scholar 7 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 8 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 8 months ago, created an answer with at least 3 up-votes. For A: Problem with downloading GSE file by GEOquery
Popular Question 8 months ago, created a question with more than 1,000 views. For How to process (seems) Agilent microarrry data?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Problem with downloading GSE file by GEOquery
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?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Problem with downloading GSE file by GEOquery
Popular Question 10 months ago, created a question with more than 1,000 views. For Some questions about call variants for mtDNA using GATK HaplotypeCaller
Popular Question 11 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 11 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 13 months ago, created a question with more than 1,000 views. For Some questions about write human mitochondrial variants into VCF file
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?

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