User: victoria_aleks

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Posts by victoria_aleks

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Comment: C: picard MarkDuplicates find EOF problem
... 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_aleks20
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Comment: C: picard MarkDuplicates find EOF problem
... 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_aleks20
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Comment: C: picard MarkDuplicates find EOF problem
... 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_aleks20
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Comment: C: picard MarkDuplicates find EOF problem
... 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_aleks20
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picard MarkDuplicates find EOF problem
... 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 ...
eof markduplicates written 4 months ago by victoria_aleks20
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Comment: C: editing phylogeny tree
... right , thank you :) ...
written 4 months ago by victoria_aleks20
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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_aleks20
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editing phylogeny tree
... 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 ...
phylogeny tree written 4 months ago by victoria_aleks20
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Comment: C: bedtools_intersect files sorting problem
... yes, and XY chromosomes a placed at the end :) ...
written 5 months ago by victoria_aleks20
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Comment: C: bedtools_intersect files sorting problem
... 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_aleks20

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