User: life99945

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life9994520
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1 year, 8 months ago
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Posts by life99945

<prev • 20 results • page 1 of 2 • next >
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IGV NullPointerException problem
... Hi! I mapped paired end library to a genome. Now I am trying to visualise it via IGV, but I am always getting this message when trying to jump to a certain chromosome: Error encountered querying alignments: java.lang.NullPointerException. Reference genome have 19 chromosomes and a lot of unplaced g ...
alignment igv written 6 days ago by life9994520
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Comment: C: wgs supercontigs (NW_XXXXXX)
... Are you meaning to align nw to nc? ...
written 5 weeks ago by life9994520
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wgs supercontigs (NW_XXXXXX)
... Hi, I have paired end reads which I mapped to a reference genome. This genome contains two types of contigs. First are contigs with NC identifiers, which represent chromosomes and second type are contigs with NW(NW_XXXXXX) identifiers, which should be supercontigs with gaps. The questions are: W ...
wgs supercontigs mapping written 5 weeks ago by life9994520
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Comment: C: Improperly paired sequences
... I just realized that Tablet divided my genome into chromosomes when I looked at 3-d column of the sam file and I can see location of the reads! Thank you! p.s. I think order of read fragments is correct, otherwise bwa said that he can not find the second pair and interrupted the process. ...
written 8 weeks ago by life9994520
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Comment: C: Improperly paired sequences
... Thank you for the answer! If this is the case, then the problem of incorrectly paired sequences disappears. However I still can’t understand on which specific part of the genome the insert was aligned. I tried to visualise with ncbi sequence viewer and IGV and it shows nothing. Only Tablet shows m ...
written 8 weeks ago by life9994520
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Improperly paired sequences
... Hi! I have a library of paired BAC end sequences, ~800bp each. Expected insertion length is 150kb. After mapping it to a reference genome I visualised results with Tablet program. The issue is that almost all of my sequences said to be "improperly paired' but despite that Tablet shows an insert l ...
tablet improperly paired sequences written 8 weeks ago by life9994520
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Comment: C: Bac-end mapping to a genome
... Ok, i will do it. Thank you! ...
written 3 months ago by life9994520
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Comment: C: Bac-end mapping to a genome
... As far as I understand what they were doing in that article is that from the pair of sequences with identity >=95% they were filtering out the shorter ones, but they didn't have reference genome, so maybe I don't need to do that. There is one moment that I don't quite understend: shouldn't i ha ...
written 3 months ago by life9994520
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Comment: A: Bac-end mapping to a genome
... Yes, those sequences are from the ends of the BAC. I will try it! ...
written 3 months ago by life9994520
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Comment: C: Bac-end mapping to a genome
... Thank you, I will try it! ...
written 3 months ago by life9994520

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