User: ifreecell

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ifreecell100
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Posts by ifreecell

<prev • 19 results • page 1 of 2 • next >
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Comment: C: Fetching Genbank Entries For List Of Accession Numbers.
... Replacing `dopt=gb` with `dopt=gbwithparts` should work, but I have not try yet. ...
written 10 months ago by ifreecell100
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Answer: A: Lastz.... using the xmask option
... The bad fasta character error come from non-ACGT characters in your fa files, to avoid this error, you just pass **"--ambiguous=iupac"** option to `lastz`, for details see [lastz documentation][1]. `lastz genome1.fa genome2.fa --ambiguous=iupac --format=maf > output.maf` [1]: http://www.bx ...
written 11 months ago by ifreecell100
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Answer: A: Fetching Genbank Entries For List Of Accession Numbers.
... I have successfully used `wget` to download more than 1000 plastid Genbank files using Accessions (with version, NC_018523.1). It's not fast, but works. mkdir -p gb fa cut -f 1 plastid.accs | while read -r acc do wget -O gb/"${acc}.gb" \ "http://www.ncbi.nlm.nih.gov/s ...
written 14 months ago by ifreecell100
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Visualization of maf alignments in JBrowse
... I have set up a local JBrowse, and very satisfied with it. However, I could not find info about how to set up a [UCSC Genome Browser-like Conservation track][1], which is a great feature for comparative analysis. Is there any way (plugin) to visualize Multiz Alignments in JBrowse? If so, how to form ...
conservation multiz alignments .maf written 15 months ago by ifreecell100 • updated 14 months ago by cmdcolin640
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Comment: C: Merge duplicate GRanges ranges
... You are right, it's just the countOverlaps() function. Thank you anyway, I will try to write a custom function. ...
written 3.0 years ago by ifreecell100
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Comment: C: Merge duplicate GRanges ranges
... There is only one chromosome in this GRanges, I don't think split() will help. I wrote the GRanges to a bed file, and it took one second for uniq -c to compute. I really appreciate it if the entire workflow can be done in Bioconductor,  is there other workaround?  ...
written 3.0 years ago by ifreecell100
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Comment: C: Merge duplicate GRanges ranges
... I am testing your approach on a sorted 5 million ranges object, it took hours before Rstudio encountered a fetal error. BTW, countOverlaps is really RAM consuming, it ate up all RAM (64G) on my computer. ...
written 3.0 years ago by ifreecell100
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Merge duplicate GRanges ranges
... Hi there, I have a GRanges object that I wanna merge duplicate ranges and append counts as a metadata columns. I know similar thing can be easily done using uniq -c, but I want do it in R/Bioconductor. Is there any suggestion? >orginalGRanges GRanges with 6 ranges and 0 metadata columns: ...
R merge granges written 3.0 years ago by ifreecell100 • updated 3.0 years ago by Devon Ryan69k
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Answer: A: Count 5'End Mapped To A Specific Genomic Position
... bedtools genomecov -d -5 -ibam input.bam -g genome.fa > output.txt More options see bedtools documents at http://bedtools.readthedocs.org/en/latest/content/tools/genomecov.html ...
written 3.0 years ago by ifreecell100
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Comment: C: annotation of duplicate reads
... Could you just give some clue? ...
written 3.0 years ago by ifreecell100

Latest awards to ifreecell

Popular Question 21 months ago, created a question with more than 1,000 views. For Merge duplicate GRanges ranges
Supporter 2.1 years ago, voted at least 25 times.
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Count 5'End Mapped To A Specific Genomic Position
Scholar 3.0 years ago, created an answer that has been accepted. For A: Count 5'End Mapped To A Specific Genomic Position
Student 3.0 years ago, asked a question with at least 3 up-votes. For Count 5'End Mapped To A Specific Genomic Position

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