User: microfuge

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microfuge1.6k
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Posts by microfuge

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Comment: C: Replace heterozygous GT to missing in vcf file using bcftools
... Not tested it but this comes to mind ` bcftools filter -S . -e 'GT=="het"' yourFile.vcf.gz` ...
written 23 hours ago by microfuge1.6k
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Comment: C: amplicon sequencing or metagenomics?
... One way I approach this is the way NCBI SRA characterizes these terms. Amplicon is classified as **strategy** in SRA and metagenomic is described as **source**. * Strategy in SRA or as described here https://www.ebi.ac.uk/ena/submit/reads-library-strategy "Amplicon sequencing: An assay in which ...
written 1 day ago by microfuge1.6k
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Comment: C: Protein symbol in output list
... For the multiple entries I presume Uniprot explains it ( https://www.uniprot.org/uniprot/P69849 ) Text from the page "There are 3 copies of the NOMO gene on chromosome 16p12-p13: NOMO1 (AC Q5JPE7), NOMO2 (AC Q5JPE7) and NOMO3. All 3 are extremely similar, which makes their individual characterizat ...
written 1 day ago by microfuge1.6k
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Comment: C: Role of large/small sample size in adjusting p-value
... My guess would be they mean low number of total tests conduced. E.g if there are fewer loci then the sum of tests done per loci aka total number of tests is few. For fewer number of total tests, multiple testing correction like Boneferroni would be too aggressive. And due to fewer number, the distri ...
written 2 days ago by microfuge1.6k
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Comment: C: Extract codon between two flanking sequences from FASTA
... This can work if the sequence is not wrapped. `perl -n -e '{if($_ =~ /CAGGCATGCC(.+)TCATCGCTGG/){print $x, $1, "\n" };$x=$_}' Test.fa` ...
written 3 days ago by microfuge1.6k
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Comment: C: Match predicted sequences to reference genome to generate data for annotation GT
... Looks like `GeMoMa` could work http://www.jstacs.de/index.php/GeMoMa . It takes in the protein sequence. ...
written 4 days ago by microfuge1.6k
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Comment: C: Calculating Effective Population Size from One Individual
... psmc seems to do that https://github.com/lh3/psmc ...
written 9 days ago by microfuge1.6k
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Answer: C: search for ORF2819
... I followed the google search links to LisSero github repo and in the source there seems to be sequence here https://github.com/MDU-PHL/LisSero/blob/master/lissero/db/sequences.fasta ...
written 14 days ago by microfuge1.6k
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Comment: C: Chip-Seq (IP-vs-Control and Mock-vs-Control) or IP-vs-Mock for peak calling
... Thanks! We have 3 replicates of each and I was surprised to see that mock has quite some enrichment although not focal so is for IP and library complexity is not very different between Mock and IP nor is the duplicate fraction. There is substantial peak overlap between (IPvsControl and MockvsContro ...
written 17 days ago by microfuge1.6k
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Chip-Seq (IP-vs-Control and Mock-vs-Control) or IP-vs-Mock for peak calling
... Dear All, I would be really grateful for your advice in this regard. In Chip-Seq where there are all 3 IP, Input and Mock how to get the best peak calls. - To run IP vs Mock and get peak calls - To have two runs IP vs Input and Mock vs Input and cancel out the peaks in mock with either bedtools ...
chip-seq written 17 days ago by microfuge1.6k

Latest awards to microfuge

Teacher 9 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Voter 10 months ago, voted more than 100 times.
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
Scholar 16 months ago, created an answer that has been accepted. For C: BedTools getfasta -split
Guru 16 months ago, received more than 100 upvotes.
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Scholar 2.1 years ago, created an answer that has been accepted. For A: Many SRR files for one experiment. What are the steps to be taken before further
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: chain file for maize
Scholar 2.1 years ago, created an answer that has been accepted. For A: Many SRR files for one experiment. What are the steps to be taken before further
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: chain file for maize
Scholar 2.1 years ago, created an answer that has been accepted. For A: Many SRR files for one experiment. What are the steps to be taken before further
Scholar 2.2 years ago, created an answer that has been accepted. For A: Many SRR files for one experiment. What are the steps to be taken before further
Commentator 2.3 years ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Tissue Specificity index (tau) should FPKM data be log transformed?
Scholar 2.9 years ago, created an answer that has been accepted. For A: Many SRR files for one experiment. What are the steps to be taken before further
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: chain file for maize
Scholar 3.0 years ago, created an answer that has been accepted. For A: Many SRR files for one experiment. What are the steps to be taken before further
Scholar 3.0 years ago, created an answer that has been accepted. For A: Many SRR files for one experiment. What are the steps to be taken before further
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: chain file for maize
Commentator 3.7 years ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
Supporter 3.7 years ago, voted at least 25 times.
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: chain file for maize

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