User: rodd

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rodd20
Reputation:
20
Status:
New User
Location:
London, United Kingdom
Last seen:
9 minutes ago
Joined:
3 years, 11 months ago
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r***************@gmail.com

Posts by rodd

<prev • 15 results • page 1 of 2 • next >
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Comment: C: How can I change the default path to which SRA files are downloaded?
... This is super easy, but you still have to extract the FASTQ files from the SRA file using fastq-dump. So it might be just easier to just use fastq-dump, changing the default save directory, according to piet's post. [UPDATE] Funny enough, just because I posted this, I changed the configuration as b ...
written 5 days ago by rodd20
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Comment: C: download all samples from a study in BioProject
... Is this command provided by piet still supposed to work? It returned an empty file for me. [UPDATE] I realised my bioproject does not have SRA files, but "biosamples" - that's why it's not working.. ...
written 4 weeks ago by rodd20
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Comment: C: Converting mapped + unmapped BAM files to raw FASTQ (RNA-seq data)
... Thank you for your answers, it helped me a lot! ...
written 3 months ago by rodd20
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Comment: C: Converting mapped + unmapped BAM files to raw FASTQ (RNA-seq data)
... Sorry, that was a typo - I did include it in my command, and have updated my previous reply. I am only outputting the reads I want to the FASTQ files, which is great. But I am still curious as to why it's removing ~1 mi reads after the BAM-FASTQ conversion, when comparing to the output of `samtools ...
written 3 months ago by rodd20
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Comment: C: Converting mapped + unmapped BAM files to raw FASTQ (RNA-seq data)
... Thank you! (Just for the record, this gave the same number of reads as when I used -F 0x900 or -F 0x100, as suggested by [finswimmer][1]. These flags are so confusing...) [1]: https://www.biostars.org/u/37605/ ...
written 3 months ago by rodd20
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Comment: C: Converting mapped + unmapped BAM files to raw FASTQ (RNA-seq data)
... Hi [finswimmer][1], Thanks you for your prompt response, and for the link to your post on samtools github. I will be following your advice (and the advice from our colleague who also responded to the thread). But just out of curiosity, I am still finding some discrepancies in the number of reads af ...
written 3 months ago by rodd20 • updated 3 months ago by finswimmer9.9k
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Comment: A: Metabolic pathways from list of protein ID numbers
... I believe what you are trying to do is an enrichment analysis. There are a multitude of similar tools to do this, but I personally use http://www.webgestalt.org/ . There may be better tools for enrichment analysis of prokaryotic genes/proteins. ...
written 3 months ago by rodd20
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Converting mapped + unmapped BAM files to raw FASTQ (RNA-seq data)
... Hi all, I need to analyse some RNA-seq data with a special aligner for repetitive elements, but the "raw" data from the cohort I am analysing came as aligned BAM files (mapped.bam + unmapped.bam files). I can obtain the raw FASTQ files from a concatenated BAM file, following [this][1] tutorial. Ho ...
bam2fastq bam fastq conversion rna-seq written 3 months ago by rodd20 • updated 3 months ago by swbarnes24.8k
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Comment: C: Selecting Random Pairs From Fastq?
... I couldn't find much information about the seqtk sample function, and I was wondering if anyone knows what happens when you choose a seed value which is too large for your original number of reads, considering the target size you set for your subsample. E.g. fastq file contains 15,000,000 reads, I ...
written 10 months ago by rodd20
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Comment: C: trimming fastq files with Trimmomatic
... Thank you so much! I will research more on this! But you definitely helped a lot already!  ...
written 3.7 years ago by rodd20

Latest awards to rodd

Supporter 3 months ago, voted at least 25 times.
Epic Question 21 months ago, created a question with more than 10,000 views. For trimming fastq files with Trimmomatic
Great Question 23 months ago, created a question with more than 5,000 views. For trimming fastq files with Trimmomatic
Popular Question 3.4 years ago, created a question with more than 1,000 views. For trimming fastq files with Trimmomatic

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