User: BM

gravatar for BM
BM60
Reputation:
60
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Trusted
Location:
United Kingdom
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2 days, 2 hours ago
Joined:
4 years, 11 months ago
Email:
b******@ucl.ac.uk

Posts by BM

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Merge fastq files
... Any help in how I would do this please? ...
written 9 days ago by BM60
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Comment: C: Merge fastq files
... So would it be printf '%s\n' *.fastq.gz | sed 's/^\([^_]*_*\).*/\1/' | uniq | while read prefix; do cat "$prefix"*R1*.fastq.gz >"${prefix}_R1.fastq.gz" cat "$prefix"*R2*.fastq.gz >"${prefix}_R2.fastq.gz" done ...
written 9 days ago by BM60
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Comment: C: Merge fastq files
... Sorry for the confusion, the original files were as you said from different lanes, e.g. A14_S90_L008_R1_001.fastq.gz Files were merged using printf '%s\n' *.fastq.gz | sed 's/^\([^_]*_[^_]*\).*/\1/' | uniq | while read prefix; do cat "$prefix"*R1*.fastq.gz >"${prefix}_R1.fas ...
written 9 days ago by BM60
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Merge fastq files
... I have RNA-seq fastq files, each sample has multiple files from different lanes: A10_S4_R1.fastq.gz A10_S8_R1.fastq.gz A10_S40_R1.fastq.gz A10_S4_R2.fastq.gz A10_S8_R2.fastq.gz A10_S40_R2.fastq.gz then A11 up A40 I am trying to merge using: cat A11*_R1.fastq.gz > A11_R1.fastq.gz This is fi ...
fastq bash merge concatenate unix written 9 days ago by BM60 • updated 9 days ago by Asaf8.1k
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Snakemake snakefile error.
... I am using code from a GitHub Snakemake repository to perform RNA-seq anlaysis on a cluster computer. The following error is giving after submission to the error: "KeyError in line 7 of /rna_seq_snakemake-master/rna_seq_snakemake-master/rna_seq.snakefile: 'species' File "/rna_seq_sna ...
snakefile github snakemake rna-seq written 11 weeks ago by BM60 • updated 11 weeks ago by RamRS27k
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Comment: C: DEXseq Error - SummarizedExperiment
... I tried what you suggested using option 1,now I have the following error: converting counts to integer mode Error in DESeqDataSet(rse, design, ignoreRank = TRUE) : all samples have 0 counts for all genes. check the counting script. ...
written 13 months ago by BM60
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DEXseq Error - SummarizedExperiment
... I have an error when performing a DEXseq count for exon usuage from RNA-seq data. DEXSeqDataSetFromSE( SE, design= ~ sample + exon + condition:exon ) I receive the error: Error in DEXSeqDataSetFromSE(SE, design = ~sample + exon + condition:exon) : make sure your SummarizedExperime ...
dexseq deseq2 rna-seq summarizedexperiment written 14 months ago by BM60 • updated 13 months ago by benformatics1.6k
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Comment: A: Directional Strand related settings for RNA-seq Analysis Software
... Yes it is Smartseq v4 Ultra low input kit ...
written 15 months ago by BM60
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Directional Strand related settings for RNA-seq Analysis Software
... A question about the library preparation for RNA-seq and Directional Strand related settings for RNA-seq Analysis Software The library was prepared was using Clontech Smartseq v4 and Nextera XT So is the library directional and first strand specific (F2R1) or second strand (F1R2)? Which libray type ...
htseq tophat rna-seq smartseq hisat2 written 15 months ago by BM60 • updated 15 months ago by Juke344.4k
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Answer: A: WGCNA error: Co-expression similarity and adjacency in Network Creation
... The count data can be transformed in DESeq2 using the variance-stabilizing transformation. The WGCNA FAQ section explains this: https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/faq.html ...
written 2.9 years ago by BM60

Latest awards to BM

Great Question 13 months ago, created a question with more than 5,000 views. For RNA-seq Anova on three groups
Great Question 13 months ago, created a question with more than 5,000 views. For Deseq2 gene name annotation
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Annotate ouput file from Deseq2
Popular Question 3.0 years ago, created a question with more than 1,000 views. For RNA-seq Anova on three groups
Popular Question 3.0 years ago, created a question with more than 1,000 views. For WGCNA error: Co-expression similarity and adjacency in Network Creation
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Annotate ouput file from Deseq2
Popular Question 4.5 years ago, created a question with more than 1,000 views. For RNA-seq Anova on three groups
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Deseq2 gene name annotation

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