User: MAPK

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MAPK1.4k
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Posts by MAPK

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How to find virus sequence with no accession information?
... I am trying to retrieve the genomic sequence of HEV71 strain VR1432 used in this study (https://www.sciencedirect.com/science/article/pii/S1074761317302224?via%3Dihub), but could not find it. I would really appreciate if someone could guide me through the appropriate resources/link. Thanks ...
genome hev71 written 5 weeks ago by MAPK1.4k • updated 5 weeks ago by genomax69k
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Comment: C: How do I find out the adaptor sequences for SRA data?
... Thank you! Not sure if I can use BBMAP if it's single ends though. ...
written 6 weeks ago by MAPK1.4k
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How do I find out the adaptor sequences for SRA data?
... I would like to analyze some small RNA data from NCBI (eg. https://www.ncbi.nlm.nih.gov/sra/SRR5593145), but I am not sure where I can find the adaptor sequences for trimming. Can anyone please suggest. ...
sra adaptor written 6 weeks ago by MAPK1.4k
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Barcode sequence for Qiime2 analysis
... Hi All, I have 16S data and I wanted to use Qiime2 to do diversity analysis. The sequencing run summary of my fastq file have barcode sequence listed as below (with + ): Lane Sample Barcode sequence PF Clusters % of the % Perfect lane barcode 1 16S_M_T1_R1_S1 GCAGGATG+ACGACAGG 47,04 ...
microbiome qiime2 written 12 weeks ago by MAPK1.4k
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Submitting R package in Bioconductor with Plink and vcftools Dependencies
... Hi All, I have written a program to analyze genotype SNP data in R and wanted to submit it as a bioconductor package. However, this package will be using Plink and vcftools and I was wondering if it is possible to submit it with such dependencies. Can someone please guide me though what I need to do ...
R bioconductor written 3 months ago by MAPK1.4k
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Comment: C: How can I analyze this data in Deseq?
... @Kevin Blighe Thanks Kevin for your answer. Yes, I wanted to look for miRNA-like reads with differential expression between samples. I have seen some papers using DESeq for these reads and wanted to give it a try. ...
written 3 months ago by MAPK1.4k
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Comment: C: How can I analyze this data in Deseq?
... This is smallRNA seq data. ...
written 3 months ago by MAPK1.4k
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How can I analyze this data in Deseq?
... I have my data called `count.mat`. count.mat <- structure(list(Sample_1 = c(2968, 1701, 272, 249, 186, 1598, 98, 9, 563, 1003, 278, 242, 137, 625, 614, 494, 681, 475, 3, 89), Sample_2 = c(2057, 1237, 339, 688, 289, 1354, 265, 17, 402, 793, 343, 267, 389, 477, 838, 663, 741 ...
rnaseq R deseq2 deseq written 3 months ago by MAPK1.4k
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Comment: C: Extract coverage from each nucleotide position of a genome in a bam file
... Thanks, does this also separate based on strand? Is there a way to sort the output according to bed file's chromosome order. My alignments in bam file are in different chromosomal order (eg. Ch16, Ch15, Ch14...Ch1). ...
written 4 months ago by MAPK1.4k
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Comment: C: Extract coverage from each nucleotide position of a genome in a bam file
... Thanks, but couldn't make this work on individual base positions. ...
written 4 months ago by MAPK1.4k

Latest awards to MAPK

Popular Question 27 days ago, created a question with more than 1,000 views. For FLT3 genes in TCGA in AML
Popular Question 27 days ago, created a question with more than 1,000 views. For Complete Genomics data analysis, pipeline version and batch effect
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Number of SNPs by target sequencing
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Reverse translate and get the genomic position
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Complete Genomics data analysis, pipeline version and batch effect
Popular Question 4 weeks ago, created a question with more than 1,000 views. For FLT3 genes in TCGA in AML
Epic Question 4 weeks ago, created a question with more than 10,000 views. For R programming, concatenate or combine all the column contents
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Complete Genomics data analysis, pipeline version and batch effect
Good Answer 7 weeks ago, created an answer that was upvoted at least 5 times. For A: How can we extract these genes from VCF file?
Appreciated 7 weeks ago, created a post with more than 5 votes. For R programming: genotype concordance
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Complete Genomics data analysis, pipeline version and batch effect
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Number of SNPs by target sequencing
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Complete Genomics data analysis, pipeline version and batch effect
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Complete Genomics data analysis, pipeline version and batch effect
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Great Question 11 weeks ago, created a question with more than 5,000 views. For R programming, concatenate or combine all the column contents
Popular Question 11 weeks ago, created a question with more than 1,000 views. For How is QUAL score calculated in multigenome VCF file?
Popular Question 3 months ago, created a question with more than 1,000 views. For Complete Genomics data analysis, pipeline version and batch effect
Popular Question 3 months ago, created a question with more than 1,000 views. For Syntax for ContEst program to identify sample contamination
Popular Question 3 months ago, created a question with more than 1,000 views. For How is QUAL score calculated in multigenome VCF file?
Popular Question 4 months ago, created a question with more than 1,000 views. For Syntax for ContEst program to identify sample contamination
Great Question 4 months ago, created a question with more than 5,000 views. For R programming, concatenate or combine all the column contents
Popular Question 4 months ago, created a question with more than 1,000 views. For Syntax for ContEst program to identify sample contamination
Popular Question 5 months ago, created a question with more than 1,000 views. For Syntax for ContEst program to identify sample contamination
Popular Question 5 months ago, created a question with more than 1,000 views. For Syntax for ContEst program to identify sample contamination

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