User: novice

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novice830
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830
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2 years, 10 months ago
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Posts by novice

<prev • 115 results • page 1 of 12 • next >
7
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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 9 months ago by novice830
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5
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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 14 months ago by novice830
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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 14 months ago by novice830
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611
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Comment: C: Increase the fifth column ( MAPQ) value in Sam file
... Good points! andthisistextfulfillsthesmartcharacterrequirement ...
written 15 months ago by novice830
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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 15 months ago by novice830
1
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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 15 months ago by novice830
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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 15 months ago by novice830
0
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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 15 months ago by novice830
0
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Answer: A: Reliable alignment tool for similar sequences of similar length other than Mumme
... From what I understand, you're looking for an aligner optimized for *split-alignment*. If that is the case, then standard BWA-SW does that. I would also recommend [YAHA](https://github.com/GregoryFaust/yaha), which I found more sensitive than BWA. Both of these support relatively large queries. ...
written 15 months ago by novice830
0
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485
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Comment: C: R loop not functional
... If you're using for-loops in R, you're doing it wrong! ...
written 15 months ago by novice830

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