User: Vladimir Bajić

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Posts by Vladimir Bajić

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Understanding flags from output of bam2cfg.pl - BreakDancer
... I followed the instructions from BreakDancer site. After creating .cfg file I examined it and I saw that I have much higher % of flag 32 than suggested.  "Manually view the insert size and flag distribution results in BRC6.cfg to see if there are any data quality issue. Usually std/mean should be & ...
flag breakdancer bam2cfg written 2.2 years ago by Vladimir Bajić0 • updated 2.2 years ago by ernfrid180
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Comment: C: CollectInsertSizeMetrics - changing DEVIATIONS gives different results -
... We don't have  coverage good enough to do de novo assembly. Anyway thanks for suggestions, it was helpful! ...
written 2.3 years ago by Vladimir Bajić0
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Comment: C: CollectInsertSizeMetrics - changing DEVIATIONS gives different results -
... So, the genomes are not that close. The estimated divergence time between them is about  8 Myr. I would definitely discard the extremities of the distribution, but the problem is that I am interested in structural rearrangements. I am trying to discover them using exactly those mate pairs that are n ...
written 2.3 years ago by Vladimir Bajić0
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Comment: C: CollectInsertSizeMetrics - changing DEVIATIONS gives different results -
... here is the histogram. I came across that paper also but I have no information about technique that company used for the insert size selection. I came in the lab and they already had everything sequence long ago. I also think that knowing the method for insert size selection would help in determinin ...
written 2.4 years ago by Vladimir Bajić0
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Comment: C: CollectInsertSizeMetrics - changing DEVIATIONS gives different results -
... I'm very new here and I have no idea why hist didn't show up (maybe there is a specific way to upload pic and I just copy-pasted it). Regarding orientation of the mapped pairs, I know that it is very important to take care of orientation when dealing with mate-paired libraries. A sequencing company ...
written 2.4 years ago by Vladimir Bajić0
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Answer: A: CollectInsertSizeMetrics - changing DEVIATIONS gives different results -
... Thank you for the answers! I didn't specify enough precisely what I did. So I'll give a bit more details, I used Bowtie2 with following parameters: sensitive local, Paired-end with the minimum fragment length for valid paired-end alignments of 1000 X 7000 and RF orientation. Sequencing company said ...
written 2.4 years ago by Vladimir Bajić0

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