User: KCC

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KCC4.0k
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I have been working in bioinformatics for two years now. About half of that time has been spent on Biostars getting great advice!

Posts by KCC

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Comment: C: Bwa On Mac : How To Run It On Terminal
... I was thinking this way was more modular as all your bioinformatics programs are in one file and you can move it easily to a new installation (if you keep all your executables in a generic location without your username in the path). You can copy the folder to a new mac, move the file in path.d to ...
written 5.9 years ago by KCC4.0k
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Answer: A: Bwa On Mac : How To Run It On Terminal
... First you need to make hidden files visible. Type this in the command line: defaults write com.apple.finder AppleShowAllFiles -bool true killall Finder You need to get the to paths.d folder. On my system, it's possible to just type "cd /private/etc/paths.d" However, you should be able to open F ...
written 5.9 years ago by KCC4.0k
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Comment: C: Why Does This The Sam Record Having A Mapping Quality Of 0
... From what I understand the XT and XA flags arise from different algorithms to the mapping quality being 0. I read this a while ago. ...
written 6.0 years ago by KCC4.0k
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Answer: A: Merge 4 Fastq Files
... Try this. Mostly default settings. Where I say "-t 4" I am assuming you have 4 processors. You can drop this number if that's not the case for you. bwa index -p mygenome -a bwtsw mygenome.fa bwa aln -t 4 bwtsw mygenome s_6_1.fastq > s_6_1.sai bwa aln -t 4 bwtsw mygenome s_6_2.fastq > s_6_ ...
written 6.1 years ago by KCC4.0k
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Comment: C: Manipulation Of Large Numbers Of Sequences Using Python Or Matlab
... If s is a string in python. Then the last five letters are just: s[-5:] So, if (sequence[-5:] == 'CATGA'): #do something ...
written 6.1 years ago by KCC4.0k
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Answer: A: How To Find Unique Reads?
... I once looked at this problem as well. I recall three ways of identifying a read that was mapped to multiple positions with BWA: 1. the presence of the characters `XT:A:R` 2. the presence of the characters `XA:Z:` 3. mapping quality (MAPQ) of 0 Based on my notes, these results all gave similar, bu ...
written 6.1 years ago by KCC4.0k • updated 5 weeks ago by RamRS24k
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Answer: A: Plotting Reads Around Tss
... Assuming you have your TSS and CpG files in BED format. You can use either a command from bedtools like intersectBED to get TSS which have CpG regions and ones that don't. Then you use an online tool like Cistrome or CEAS to get a profile across your BED regions. Sorry, I can't be more specific a ...
written 6.1 years ago by KCC4.0k
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Comment: C: Is It Okay To Remove Chrun And Chr*_Random Reads From A Bed File?
... I would also support keeping them for alignment. The reason for me is that if I don't, I might get extra reads mapping to the main chromosomes when they would otherwise have mapped to the rermoved sequences. However, for certain operations like peak calling in DNA-seq, I remove them as I think th ...
written 6.1 years ago by KCC4.0k
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Answer: A: Isn'T A Prokaryotic Gene Continuous..?
... The CDS is the coding DNA sequence, meaning it's the part of the genetic sequence that gets directly translated into a protein. Since a single gene can code for multiple proteins, there can be multiple CDS regions. For genes, that contain introns which do not code for protein sequence, this means ...
written 6.3 years ago by KCC4.0k
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Comment: C: Is There A Realtime Molecular Clock Within The Genome To Co-Ordinate The Develop
... Hi rammanohardr. Welcome to Biostars! We focus on bioinformatics methodology. Your question sounds like a purely biological question and seems to be off topic here. Luckily, there is a very similar question-and-answer site for biological questions: http://biology.stackexchange.com/ ...
written 6.3 years ago by KCC4.0k

Latest awards to KCC

Autobiographer 5.9 years ago, has more than 80 characters in the information field of the user's profile.
Guru 5.9 years ago, received more than 100 upvotes.
Centurion 5.9 years ago, created 100 posts.
Voter 5.9 years ago, voted more than 100 times.
Supporter 5.9 years ago, voted at least 25 times.
Good Answer 6.5 years ago, created an answer that was upvoted at least 5 times. For A: Looking For People That Would Try A Custom Genome Viewer That I Wrote For Bioinf
Good Answer 6.6 years ago, created an answer that was upvoted at least 5 times. For A: Converting Python Code To R
Good Answer 6.6 years ago, created an answer that was upvoted at least 5 times. For A: Is Biostar Killing The Bioinformatics Core?
Commentator 6.8 years ago, created a comment with at least 3 up-votes. For C: Statistical Challenges For Analyzing Ngs Data?
Commentator 6.8 years ago, created a comment with at least 3 up-votes. For C: How Has Bioinformatics Improved Over Time?
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Teacher 6.9 years ago, created an answer with at least 3 up-votes. For A: Output Of Chip-Seq Data Analysis Using Macs
Teacher 6.9 years ago, created an answer with at least 3 up-votes. For A: How To Identify The Protein Domains Of A Specific Protein?
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