User: camerond

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camerond150
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Cardiff
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Posts by camerond

<prev • 38 results • page 1 of 4 • next >
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Comment: C: Snakemake - moving, re-naming, unzipping and merging files for downstream analys
... I understand that. The issue is that the `/path/to/file/` and `filenames` of the original 120 files have no consistency. This was the main reason for using pandas in the first rule, in order to standardise, or to use your term, normalise the sample/filenames so that I could start using the typical ` ...
written 5 weeks ago by camerond150
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Comment: C: Snakemake - moving, re-naming, unzipping and merging files for downstream analys
... Ah ... I didn't know that. Thanks for the heads up! ...
written 5 weeks ago by camerond150
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Comment: C: Snakemake - moving, re-naming, unzipping and merging files for downstream analys
... No probs. Fair points. Most of the snakemake walkthrough/tutorials describe the functionality of `{wildcards}` in relation to a single `{wildcard}` that remains constant and flows through the most, if not all of the rules i.e. `{sample}`. I've yet to find one that describes the best way do deal with ...
written 5 weeks ago by camerond150
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Comment: C: Snakemake - moving, re-naming, unzipping and merging files for downstream analys
... Response to first post: Probably, yes. However, I was hoping to standardise the `{wildcards}` across the rules. Your suggestion would add more `{wildcards}`, but that may be the cleanest way to do it. What do you mean pandas may be overkill? What would you suggest as an alternative? ...
written 5 weeks ago by camerond150
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Comment: C: Snakemake - moving, re-naming, unzipping and merging files for downstream analys
... Thanks for your suggestions. Re: if statement - Although I think both work, your way is less verbose so I have changed it in the IP. ...
written 5 weeks ago by camerond150
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Snakemake - moving, re-naming, unzipping and merging files for downstream analysis
... In my current project, I have ~560 RNA-seq fastq files (120 samples) that were sequenced in various locations. As such, the naming structure of the files are different, some files are zipped and some are unzipped, the files are dotted around our databank in various locations and the sample ID for ea ...
merging fastq snakemake python written 6 weeks ago by camerond150
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Comment: C: Extracting high quality reads from partially failed 10X single cell RNA-, ATAC-s
... No probs. Many Thanks. ...
written 5 months ago by camerond150
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Comment: C: Extracting high quality reads from partially failed 10X single cell RNA-, ATAC-s
... I'm hoping only half the reads will have Ns in them. I'll def filter these out first. Many thanks for the suggestion. ...
written 5 months ago by camerond150
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Comment: C: Extracting high quality reads from partially failed 10X single cell RNA-, ATAC-s
... Many Thanks @ATpoint. I will try this on Monday. The problem is actually with the R2 reads. The R1 reads are consistently 28bp long. I tried running the files through cell ranger to see what would happen but, in their current state, the software does not recognise the 10X chemistry used in the exper ...
written 5 months ago by camerond150
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Comment: C: Extracting high quality reads from partially failed 10X single cell RNA-, ATAC-s
... We have contacted them, but unfortunately our service contract with the Hiseq 4000, has just ended (we are moving over to the Novaseq for future runs), so I'm not sure we'll get, or whether it's worth getting, anything back from them. We were running this experiment as a test on the samples to see i ...
written 5 months ago by camerond150

Latest awards to camerond

Popular Question 12 weeks ago, created a question with more than 1,000 views. For Get rsID for a list of SNPs in an entire GWAS sumstats file
Great Question 5 months ago, created a question with more than 5,000 views. For Extract ONLY chromosomes 1-22 from bam file - removing extraneous chr annotations
Student 11 months ago, asked a question with at least 3 up-votes. For Extract ONLY chromosomes 1-22 from bam file - removing extraneous chr annotations
Popular Question 14 months ago, created a question with more than 1,000 views. For Extract ONLY chromosomes 1-22 from bam file - removing extraneous chr annotations
Supporter 14 months ago, voted at least 25 times.
Scholar 15 months ago, created an answer that has been accepted. For A: Snakemake logging error
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Snakemake logging error
Popular Question 24 months ago, created a question with more than 1,000 views. For Get rsID for a list of SNPs in an entire GWAS sumstats file
Popular Question 24 months ago, created a question with more than 1,000 views. For Extract ONLY chromosomes 1-22 from bam file - removing extraneous chr annotations

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