User: tim.ivanov.92

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Posts by tim.ivanov.92

<prev • 57 results • page 1 of 6 • next >
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Comment: C: Annotating multiple sequence alignment
... ok, thank you anyway! ...
written 14 days ago by tim.ivanov.9210
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Comment: C: Annotating multiple sequence alignment
... Thank you, this is helpful! Would you mind giving me an example of usage please? ...
written 16 days ago by tim.ivanov.9210
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Annotating multiple sequence alignment
... Does anyone know know how to use [TEXshade][1] package? Specifically, i want to just highlight some specific regions inside my alignment (exons) [1]: http://ctan.math.utah.edu/ctan/tex-archive/macros/latex/contrib/texshade/texshade.pdf ...
maf texshade alignment written 17 days ago by tim.ivanov.9210 • updated 17 days ago by Asaf5.2k
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Comment: C: Convert MAF to FASTA
... Thank you for the second link - i'll look into it Do you mb know how to get complete UCSC fasta records by **droSec1.super_9**? I think i will need it anyway later ...
written 8 weeks ago by tim.ivanov.9210
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Comment: C: Convert MAF to FASTA
... Does it considerer blocks inside an alignment? cos thats the whole problem - different blocks may include different organisms ...
written 8 weeks ago by tim.ivanov.9210
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Convert MAF to FASTA
... I've obtained multiple MAF files through UCSC. And i really want to be able to convert them into fasta files. Is there a tool for it? I found this github [https://github.com/dentearl/mafTools/][1] which has mafToFastaStitcher tool, but the description says that it requires complete fasta records to ...
alignment soft ucsc written 8 weeks ago by tim.ivanov.9210 • updated 8 weeks ago by kloetzl1.0k
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Answer: A: MAF format help
... In case anyone else will also encounter this problem: mafFrag doesn't provide regions of genomes in the alignment. to get them, you will have to use **mafsInRegion** tool: $ mafsInRegion mafsInRegion - Extract MAFS in a genomic region usage: mafsInRegion regions.bed out.maf|out ...
written 11 weeks ago by tim.ivanov.9210
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Comment: C: MAF format help
... its The October 2005 Drosophila persimilis genome assembly, which was produced by the Broad Institute at MIT and Harvard. ([link][1]) It looks like there is no chromosomal assembly for this fly - only contigs Thank you anyway for your help! [1]: https://genome.ucsc.edu/cgi-bin/hgTracks?chromInf ...
written 12 weeks ago by tim.ivanov.9210
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Comment: C: MAF format help
... Thank you again! I'm getting weird results checking the alignment region: I've done blat of a droPer1's region from the alignment, and i got this hit: browser details YourSeq 1377 1 1377 1377 100.0% super_68 - 78837 80213 1377 What is this super_68 chromosome? ...
written 12 weeks ago by tim.ivanov.9210
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IGV browser for mafFrag output
... Is there a way to open output files from mafFrag into [integrative genome viewer][1]? I need to visualize output from mafFrag tool, and IGV seems like a tool to do it, but when i import my *.maf file i don't see the alignment at my region, all i see are labels on the left (see screenshot) [screens ...
maf maffrag igv written 12 weeks ago by tim.ivanov.9210

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