User: tim.ivanov.92

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Posts by tim.ivanov.92

<prev • 51 results • page 1 of 6 • next >
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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 17 days 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 21 days 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 22 days 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 22 days ago by tim.ivanov.9210
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Comment: A: MAF format help
... Also an additional question: Is there a way to visualize maf file? i've tried IGV browser, but it seems to fail importing the alignment. ...
written 23 days ago by tim.ivanov.9210
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Comment: C: MAF format help
... Thank you for your answer and links - that helps a lot! But why in my example the chromosome is 1? Did you mean 2L - the same as dm3? ...
written 23 days ago by tim.ivanov.9210
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MAF format help
... Does anyone know the format of *.MAF files generated my ucsc tools mafFrags and mafFrafg? i've ran a command: mafFrags -refCoords dm3 multiz15way dm3_mrp1.bed mrp1_maffrags.maf where dm3_mrp1.bed contain just one line: chr2L 12727116 12737959 mrp1_dm3 1 + wh ...
maffrags ucsc written 24 days ago by tim.ivanov.9210
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Comment: C: SRA archive metadata
... Thank you for your reply! I've actually trying to obtain metadata for already downloaded files (they are controlled, but i have a key) Can you specify what is it that i see in the output of your request? each line is like: > SRR7944888,2018-09-30 18:41:15,2018-09-30 > 18:26:12,11129735,153 ...
written 5 weeks ago by tim.ivanov.9210
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SRA archive metadata
... I'm using this command esearch -db sra -query SRR1399843 | efetch -format runinfo To obtain metadata about SRA archive. it results in such information: > Run SRR1399843 > > ReleaseDate 2014-06-14 13:41:56 > > LoadDate 2014-10-04 03:42:33 > > spots 40704619 > ...
ncbi sra sra-toolkit written 5 weeks ago by tim.ivanov.9210 • updated 5 weeks ago by vkkodali600
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Comment: C: Get gene counts from *.sam file and annotation
... thats not really solving my problem, i first need to use something like bedtools intersect ...
written 9 weeks ago by tim.ivanov.9210

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