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Moderator: Biomonika (Noolean)

gravatar for Biomonika (Noolean)
Reputation:
3,080
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Trusted
Location:
State College, PA, USA
Website:
http://sites.psu.edu/b...
Twitter:
biomonika
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Google Scholar Page
Last seen:
3 months ago
Joined:
8 years, 1 month ago
Email:
m*****************@gmail.com

Bioinformatics of sequences. Sex chromosomes. Enjoying DNA in my computer.

“I'm fascinated by the idea that genetics is digital. A gene is a long sequence of coded letters, like computer information. Modern biology is becoming very much a branch of information technology.”

Richard Dawkins

Posts by Biomonika (Noolean)

<prev • 465 results • page 1 of 47 • next >
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Comment: C: positive selection project
... What's your timeline for this project? Are you a student? How did you choose this project? You cannot ultimately prove positive selection, only have strong evidence. It will be frustrating to work on this without help, so I would consider switching projects/professors. ...
written 2.1 years ago by Biomonika (Noolean) ♦ 3.1k
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Comment: C: WGS data for healthy human women sequenced on Illumina HiSeq 2000?
... Thank you, this is exactly what I was looking for. ...
written 2.1 years ago by Biomonika (Noolean) ♦ 3.1k
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WGS data for healthy human women sequenced on Illumina HiSeq 2000?
... I need to download WGS for healthy women, ideally sequenced on Illumina HiSeq 2000. I intitially looked into 1000G data ([http://www.internationalgenome.org/data/][1]), but it doesn't seem to specify which machine was used for sequencing. I am interested in low complexity sequences and thus worried ...
1000g wgs illumina hiseq written 2.1 years ago by Biomonika (Noolean) ♦ 3.1k • updated 20 months ago by Biostar ♦♦ 20
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Comment: C: Selecting Random Pairs From Fastq?
... That's random seed. Same seed ensures same "random" results (useful for reproducibility). ...
written 2.2 years ago by Biomonika (Noolean) ♦ 3.1k
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Comment: C: StackExchange/Area51 bioinformatics is back
... Actually I don't read SeqAnswers because I miss threads there. That's the only reason. I have spent last 5 years on Biostars though. ...
written 2.5 years ago by Biomonika (Noolean) ♦ 3.1k
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mpileup for PacBio reads
... I am interested in **calling errors** (especially indels) in my **PacBio alignments**. I want ALL errors to be reported, not only high frequency ones. Thus, the best for me would an alternative to mpileup for Illumina reads. I am considering two options here: **1) using PacBio-specific software**, ...
quiver calling pacbio mpileup variants written 2.6 years ago by Biomonika (Noolean) ♦ 3.1k • updated 23 months ago by tjduncan • 250
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Comment: C: How To Split A Multiple Fasta
... I can show an example. These commands worked for me: `csplit panTro5.fa /\>chr.*/ {*}` followed by `for a in x*; do echo $a; mv $a $(head -1 $a).txt; done;` As you said, very convenient on machines other than yours. ...
written 2.7 years ago by Biomonika (Noolean) ♦ 3.1k
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Comment: C: avoid within table correlations in rcorr
... What specifically do you call within table correlation? ...
written 2.8 years ago by Biomonika (Noolean) ♦ 3.1k
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Comment: C: Align short reads to multifasta reference - cant see in IGV
... First import your multiref.fasta as a genome and only then load your bam file. ...
written 2.8 years ago by Biomonika (Noolean) ♦ 3.1k
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Answer: A: what do read with blue outline represent in IGV?
... Could [this][1] page help? ![for an inferred insert size that is smaller than expected (insertion)][2] [igv/interpreting_insert_size][3] [1]: http://software.broadinstitute.org/software/igv/interpreting_insert_size [2]: http://software.broadinstitute.org/software/igv/sites/cancerinformatics.o ...
written 2.8 years ago by Biomonika (Noolean) ♦ 3.1k

Latest awards to Biomonika (Noolean)

Popular Question 23 months ago, created a question with more than 1,000 views. For How To Assemble Chloroplast Genome?
Good Question 23 months ago, asked a question that was upvoted at least 5 times. For Fastq Format Confusion
Great Question 23 months ago, created a question with more than 5,000 views. For Blast 2.25+ Segmentation Fault When -Outfmt Set To 6,7 Or 10
Appreciated 23 months ago, created a post with more than 5 votes. For C: Diagnose my daughter?
Epic Question 23 months ago, created a question with more than 10,000 views. For How To Extract Set Of Reads From Fastq (Or Eventually Fasta And Qual) Based On List Of Ids?
Epic Question 23 months ago, created a question with more than 10,000 views. For Coverage In Bam File - Bases And Overall Count
Popular Question 23 months ago, created a question with more than 1,000 views. For Where to download raw HGDP data used for population genetics studies
Popular Question 23 months ago, created a question with more than 1,000 views. For Software to calculate expected sequence identity between two species, given speciation time
Popular Question 23 months ago, created a question with more than 1,000 views. For How to generate bam files for Quiver
Appreciated 23 months ago, created a post with more than 5 votes. For C: Do bioinformaticians often break molecular biologists' hearts by being the first
Great Question 23 months ago, created a question with more than 5,000 views. For How To Assemble Chloroplast Genome?
Popular Question 23 months ago, created a question with more than 1,000 views. For Mapping mate-pairs reads with bowtie2
Popular Question 23 months ago, created a question with more than 1,000 views. For span of GFF file
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Student 23 months ago, asked a question with at least 3 up-votes. For How To Assemble Chloroplast Genome?
Popular Question 23 months ago, created a question with more than 1,000 views. For reviewing a paper with software/code I cannot run
Popular Question 23 months ago, created a question with more than 1,000 views. For Where Can I Download Annotated Transposable Elements From Arabidopsis Together With Their Location On Chromosomes?
Popular Question 23 months ago, created a question with more than 1,000 views. For How to generate bam files for Quiver
Popular Question 23 months ago, created a question with more than 1,000 views. For Where Can I Download Annotated Transposable Elements From Arabidopsis Together With Their Location On Chromosomes?
Great Question 23 months ago, created a question with more than 5,000 views. For Blast 2.25+ Segmentation Fault When -Outfmt Set To 6,7 Or 10
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