User: BM

gravatar for BM
BM60
Reputation:
60
Status:
Trusted
Location:
United Kingdom
Last seen:
4 days, 14 hours ago
Joined:
5 years, 3 months ago
Email:
b******@ucl.ac.uk

Posts by BM

<prev • 21 results • page 1 of 3 • next >
0
votes
1
answer
238
views
1
answers
Comment: C: Merge fastq files
... Any help in how I would do this please? ...
written 3 months ago by BM60
0
votes
1
answer
238
views
1
answers
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 3 months ago by BM60
0
votes
1
answer
238
views
1
answers
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 3 months ago by BM60
0
votes
1
answer
238
views
1
answer
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 3 months ago by BM60 • updated 3 months ago by Asaf8.4k
2
votes
0
answers
303
views
0
answers
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 6 months ago by BM60 • updated 6 months ago by RamRS30k
0
votes
1
answer
629
views
1
answers
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 17 months ago by BM60
0
votes
1
answer
629
views
1
answer
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 17 months ago by BM60 • updated 17 months ago by benformatics2.0k
0
votes
2
answers
577
views
2
answers
Comment: A: Directional Strand related settings for RNA-seq Analysis Software
... Yes it is Smartseq v4 Ultra low input kit ...
written 18 months ago by BM60
0
votes
2
answers
577
views
5 follow
2
answers
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 18 months ago by BM60 • updated 18 months ago by Juke344.8k
1
vote
2
answers
2.6k
views
2
answers
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 3.2 years ago by BM60

Latest awards to BM

Great Question 17 months ago, created a question with more than 5,000 views. For RNA-seq Anova on three groups
Great Question 17 months ago, created a question with more than 5,000 views. For Deseq2 gene name annotation
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Annotate ouput file from Deseq2
Popular Question 3.3 years ago, created a question with more than 1,000 views. For RNA-seq Anova on three groups
Popular Question 3.3 years ago, created a question with more than 1,000 views. For WGCNA error: Co-expression similarity and adjacency in Network Creation
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Annotate ouput file from Deseq2
Popular Question 4.8 years ago, created a question with more than 1,000 views. For RNA-seq Anova on three groups
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Deseq2 gene name annotation

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1510 users visited in the last hour