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 11 days 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 11 days 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 11 days 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 11 days 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 11 days ago by
victoria_aleks • 20
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Comment:
C: editing phylogeny tree
... right , thank you :) ...
written 15 days 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 15 days 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 16 days ago by
victoria_aleks • 20
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... yes, and XY chromosomes a placed at the end :) ...
written 5 weeks 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 weeks ago by
victoria_aleks • 20
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