User: novice

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novice980
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Posts by novice

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Comment: C: Any published data with known percentage of virus sequences?
... Thanks, but these were determined using novel methods. I am wondering how such methods are verified if there are no samples with experimentally-known viral abundance. ...
written 22 months ago by novice980
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Any published data with known percentage of virus sequences?
... Hello, I have a few assumptions I would like to test about viral data. Would anyone be familiar with published papers that have experimentally (or somehow) determined the percentage of viral sequences in the data? I have looked into some HMP samples but couldn't that list the percentage of virus e ...
metagenomics next-gen written 22 months ago by novice980
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Answer: A: How to repair *all* problems identified by FastQC?
... Easy: You download the tool FixReadsForGood.pl and select option `--no-more-worries`. Just kidding! Yes, there are usually some warnings that you can ignore. Quality control is entirely based on your knowledge of the sequences and your purposes. In my opinion, people more often than not unnecess ...
written 2.7 years ago by novice980
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Comment: C: Processing FASTA files
... > fgrep -o > sequence.fasta | wc -l This doesn't work because the `>` is a special character on the command-line; it redirects standard output into a file. You have to use single or double quotations as proposed below. ...
written 3.1 years ago by novice980
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Answer: A: Editing header of a fasta file
... I think the answer above is safe and correct. Here's a `sed` solution that is less safe (we don't know what is changing between the headers): ``` $ cat old.fasta | sed 's/>.*:\(M[0-9]*\):.*/>\1/' > new.fasta ``` Edit: excluded colons from headers. ...
written 3.1 years ago by novice980
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Comment: C: Increase the fifth column ( MAPQ) value in Sam file
... Good points! andthisistextfulfillsthesmartcharacterrequirement ...
written 3.1 years ago by novice980
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Comment: C: Increase the fifth column ( MAPQ) value in Sam file
... You can use `awk -i inplace -v OFS='\t' '$5 += 7' alignment.sam`, but it's good practice to keep your original files. This is what I would do: `cat alignment.sam | awk -v OFS='\t' '$5 += 7' > alignment_mapqincreasedbyseven.sam` ...
written 3.1 years ago by novice980
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Answer: A: Increase the fifth column ( MAPQ) value in Sam file
... Hi madhu.9124, Such tasks are typically done using `awk` or `perl`. Here's one solution: ``` cat alignment.sam | awk -v OFS='\t' '$5 += 7' ``` This will increase MAPQ (field 5) by 7. ...
written 3.1 years ago by novice980
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Answer: A: Extracting Features That Appear In TSS Regions
... Hi armonazizi, From my experience, TSS are not explicitly annotated. In fact, they are usually impossible to identify, but I don't know about mm10. Take a look at the annotation file, and decide what feature you want to select. Let's say the features you want have the 3rd column saying 'transcript' ...
written 3.1 years ago by novice980
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Comment: C: samtools view region
... No, it is not possible with samtools. You will need to write a script and work with the sam file for your purpose. ...
written 3.1 years ago by novice980

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Good Answer 2.1 years ago, created an answer that was upvoted at least 5 times. For A: How to repair *all* problems identified by FastQC?
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