User: microfuge

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microfuge1.8k
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Posts by microfuge

<prev • 296 results • page 1 of 30 • next >
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Comment: C: GNU parallel command with several multiple arguments
... Sure. As per how I understand it, it is easiest to first print what gnuparallel sees and then cherrypick the argument numbers. `parallel --dry-run -N 2 command -t {} ::: 4 8 ::: File1 File2 File3 File4 ` will return ``` command -t 4 File1 4 File2 command -t 4 File3 4 File4 command -t 8 File1 8 ...
written 10 weeks ago by microfuge1.8k
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Answer: C: GNU parallel command with several multiple arguments
... I think arguments can be grouped by `-N ` argument. `parallel --dry-run -N 2 command -t {1} {2} {4} {1}_{2}.out ::: 4 8 ::: File1 File2 File3 File4 ` ...
written 10 weeks ago by microfuge1.8k
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Comment: C: How to handle hexaploidy of Wheat for vcf file
... One way (only my guess) would be to look at genotypes/info available in ensembl plants website for wheat ( https://plants.ensembl.org/Triticum_aestivum/Info/Index a quote from the website "Bread wheat is hexaploid, with a genome size estimated at ~17 Gb, composed of three closely-related and indepen ...
written 10 weeks ago by microfuge1.8k
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Comment: C: inclusion or exclusion in gff by list of chromosomes/scaffolds
... Just thinking but can bedtools intersect work ? It takes in a gff3 file. They bed can be `chrname 0 chrlen` of required chromosomes. ...
written 11 weeks ago by microfuge1.8k
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Comment: C: retrieve a table of genes for mouse
... I find the UCSC tables a bit confusing. An alternate and easier (I think) way would be to use ensembl biomart https://www.ensembl.org/biomart/martview/ . You can select database -> ensembl genes . Dataset -> human/mouse genes. Then clicking attributes (on the left pane) -> External . Ther ...
written 11 weeks ago by microfuge1.8k
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Comment: C: Finding gene ontology terms for a list of genes
... You can try out this perl one liner. It splits the second field by `|` then again by `=` to get the gene name, then appends the GO to each with a tab. In the end prints gene with GO categories. `perl -lane 'BEGIN{%store}{my %store=map {$store{[split /=/,$_]->[-1]}.="\t".$F[0]} (split /\|/,$F[1] ...
written 11 weeks ago by microfuge1.8k
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Comment: C: Why the sequences are completely different with the same position in 1000 genome
... I guess, the reads are soft clipped so the clipped sequences are in the read sequence. You can cut out first 13 bases of read1, first 40 bases of read2 and first 22 bases of read3 in your example. ...
written 11 weeks ago by microfuge1.8k
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Comment: C: Why are there regions missing from mappability tracks provided by UCSC?
... I presume these are stretches of `Ns` in the reference. ...
written 11 weeks ago by microfuge1.8k
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Comment: C: retrieve a table of genes for mouse
... As far as I know there is no option to sort it from the server side. ...
written 11 weeks ago by microfuge1.8k
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Answer: C: retrieve a table of genes for mouse
... The UCSC table browser can be used directly * in UCSC mm10 genome * Tools -> table browser -> group (genes and gene predictions) -> track (gencode VM23) * In output format dropdown list (select fields from primary and related tables) * Click get output * in mm10 kgxref fields (check radio ...
written 11 weeks ago by microfuge1.8k

Latest awards to microfuge

Teacher 3 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Scholar 3 months ago, created an answer that has been accepted. For C: BedTools getfasta -split
Scholar 3 months ago, created an answer that has been accepted. For C: BedTools getfasta -split
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Voter 14 months ago, voted more than 100 times.
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
Scholar 20 months ago, created an answer that has been accepted. For C: BedTools getfasta -split
Guru 20 months ago, received more than 100 upvotes.
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: chain file for maize
Scholar 2.4 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 2.4 years ago, created an answer with at least 3 up-votes. For A: chain file for maize
Scholar 2.4 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 2.4 years ago, created an answer with at least 3 up-votes. For A: chain file for maize
Scholar 2.4 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 2.5 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 2.6 years ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Tissue Specificity index (tau) should FPKM data be log transformed?
Scholar 3.2 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
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: chain file for maize
Scholar 3.3 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 3.3 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

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