User: victoria_aleks
victoria_aleks • 20
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Posts by victoria_aleks
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... thank you for your advice!
the original .bam files i have downloaded from a cancer database, they are kind of old and theoretically could be processed by the old version. I ran 'bedtools intersect' on these files to produce new "intersected" .bam files. That means that my new .bams will have EOF any ...
written 4 months ago by
victoria_aleks • 20
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... well, now i have tried to convert my bam into sam, ant then into bam again, and that way MarkDuplicates worked. I guess, I have to repeat this elabortae procedure for each of files... sad :) ...
written 4 months ago by
victoria_aleks • 20
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... thank you! is there a way to find out what is wrong then? because all the files are of the size I would expect and when I calculate read depth from these files it looks good and normal. and i have 150 these files... so, really really dont want to trash them and start everything from the beginning:) ...
written 4 months ago by
victoria_aleks • 20
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... can it be that it was produced by the older software version, thats why it has no EOF? or is it not the problem of EOF after all? ...
written 4 months ago by
victoria_aleks • 20
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... Dear all,
I am running picard MarkDuplicates but getting the error "Exception in thread "main" htsjdk.samtools.FileTruncatedException: Premature end of file:...". And it does not produce any output files.
I tried picard's SortSam by coordinates - did not help. Then I added EOF to the .bam file by ...
written 4 months ago by
victoria_aleks • 20
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Comment:
C: editing phylogeny tree
... right , thank you :) ...
written 4 months ago by
victoria_aleks • 20
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Comment:
C: editing phylogeny tree
... yes, everything works perfectly with other types of tree, but I d prefer the unrooted. Cartoon works neither...
thank you for the advice , though:) ...
written 4 months ago by
victoria_aleks • 20
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... Dear all,
I need to edit my tree, i.e.: change color of particular labels (branch tips), collapse few branches - and do it on UNROOTED (radiated) tree. I have tried FigTree - and, apparently, it does not allow to collaps branches in the regime of unrooted tree (?!); then I have tried MEGA - i can n ...
written 4 months ago by
victoria_aleks • 20
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... yes, and XY chromosomes a placed at the end :) ...
written 5 months ago by
victoria_aleks • 20
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... I actually sorted the bed file in this manner, but it puts the XY at the end, while my bam file has XY chromosomes in between single-number chromosomes and double-number chromosomes (i.e. between chr9 and chr10) ...
written 5 months ago by
victoria_aleks • 20
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