Moderator: Biomonika (Noolean)

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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 • 462 results • page 1 of 47 • next >
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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 24 days 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 4 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 5 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 6 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 7 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 7 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 7 months ago by Biomonika (Noolean)3.0k
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Comment: C: Who is an appropriate person to ask for references while applying for PhD?
... I would go for diversity. In ideal case, both 1 and 2 + definitely somebody from your current job, ideally boss. ...
written 7 months ago by Biomonika (Noolean)3.0k
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Comment: C: Where does my RNASeq contamination fits on the Tree of Life?
... Can you point me to such list/database? ...
written 8 months ago by Biomonika (Noolean)3.0k
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Where does my RNASeq contamination fits on the Tree of Life?
... I have **RNASeq of algal cultures** so my samples are not really axenic. Instead, the presence of some bacteria or fungus is to be expected. I assembled my reads with Trinity and now I would like to estimate the origin of each individual contig. Ideally, I would like to get **visualization of where ...
species algae contamination rna-seq written 8 months ago by Biomonika (Noolean)3.0k

Latest awards to Biomonika (Noolean)

Appreciated 3 months ago, created a post with more than 5 votes. For C: Diagnose my daughter?
Popular Question 5 months ago, created a question with more than 1,000 views. For Is Target Site Duplication Part Of Repeatmasker Annotation?
Good Question 5 months ago, asked a question that was upvoted at least 5 times. For Visualize Insert Size For Mate-Pairs And Calculate Statistics
Great Question 5 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
Teacher 7 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
Scholar 7 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
Popular Question 9 months ago, created a question with more than 1,000 views. For Is Target Site Duplication Part Of Repeatmasker Annotation?
Teacher 10 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 10 months ago, created a question with more than 1,000 views. For How To Visualise Newbler Output?
Great Question 10 months ago, created a question with more than 5,000 views. For Coverage In Bam File - Bases And Overall Count
Popular Question 11 months ago, created a question with more than 1,000 views. For Does Information About Coverage Covers Diploid Or Haploid Size Of Genome?
Appreciated 12 months ago, created a post with more than 5 votes. For C: Diagnose my daughter?
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
Appreciated 14 months ago, created a post with more than 5 votes. For C: Diagnose my daughter?
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: Reliable Online Ssh
Good Question 14 months ago, asked a question that was upvoted at least 5 times. For Final Solution For "Mapq Should Be 0 For Unmapped Read."
Scholar 18 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 18 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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