Moderator: Biomonika (Noolean)

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State College, PA, USA
Website:
http://sites.psu.edu/b...
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biomonika
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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 4 weeks ago by Biomonika (Noolean)3.0k
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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 6 weeks ago by Biomonika (Noolean)3.0k
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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 6 weeks ago by Biomonika (Noolean)3.0k • updated 6 weeks ago by ATPoint2.5k
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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 12 weeks ago by Biomonika (Noolean)3.0k
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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 6 months ago by Biomonika (Noolean)3.0k
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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 7 months ago by Biomonika (Noolean)3.0k
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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 9 months ago by Biomonika (Noolean)3.0k
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Comment: C: avoid within table correlations in rcorr
... What specifically do you call within table correlation? ...
written 9 months ago by Biomonika (Noolean)3.0k
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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 9 months ago by Biomonika (Noolean)3.0k
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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 9 months ago by Biomonika (Noolean)3.0k

Latest awards to Biomonika (Noolean)

Great Question 8 days 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 5 months ago, created a post with more than 5 votes. For C: Diagnose my daughter?
Popular Question 7 months ago, created a question with more than 1,000 views. For Is Target Site Duplication Part Of Repeatmasker Annotation?
Good Question 7 months ago, asked a question that was upvoted at least 5 times. For Visualize Insert Size For Mate-Pairs And Calculate Statistics
Great Question 7 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
Scholar 9 months ago, created an answer that has been accepted. For A: How to find out the reverse complement of DNA from each FASTA formated sequence
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How to find out the reverse complement of DNA from each FASTA formated sequence
Popular Question 11 months ago, created a question with more than 1,000 views. For Is Target Site Duplication Part Of Repeatmasker Annotation?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How to find out the reverse complement of DNA from each FASTA formated sequence
Popular Question 12 months ago, created a question with more than 1,000 views. For How To Visualise Newbler Output?
Great Question 12 months ago, created a question with more than 5,000 views. For Coverage In Bam File - Bases And Overall Count
Popular Question 13 months ago, created a question with more than 1,000 views. For Does Information About Coverage Covers Diploid Or Haploid Size Of Genome?
Appreciated 14 months ago, created a post with more than 5 votes. For C: Diagnose my daughter?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: How to find out the reverse complement of DNA from each FASTA formated sequence
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