User: victoria_aleks

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Posts by victoria_aleks

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Comment: C: bedtools_intersect files sorting problem
... yes, and XY chromosomes a placed at the end :) ...
written 4 days ago by victoria_aleks0
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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 4 days ago by victoria_aleks0
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Comment: C: bedtools_intersect files sorting problem
... I still dont understand how i can reshape the order of the chromosomes, so that X and Y will be not between chr9 and chr10, but at the beginning/or at the end... ...
written 4 days ago by victoria_aleks0
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Comment: C: bedtools_intersect files sorting problem
... the error is that genome file and bed file have sorting "1 2 3 4 5 6 7 8 9 10 11... x y" and bam file has " 1 2 3 4 5 6 7 8 9 x y 11 12..." ...
written 4 days ago by victoria_aleks0
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Comment: C: bedtools_intersect files sorting problem
... I did not. I have sorted bed and genome files according to bam (as I thought). only later I found out that bam file has this strange sorting with XY chromosomes, and, honestly, i dont know how to sort bam file :) ...
written 4 days ago by victoria_aleks0
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bedtools_intersect files sorting problem
... Dear all, I am running the command: bedtools intersect -sorted -g [GENOME_FILE] -abam [BAM_FILE] -b [BED_FILE] > [OUTPUT_FILE] - and am getting an error about wrong sorting. Apparently my input BAM files have strange sorting, that goes: chr1 chr2 ... Chr9 X Y Chr11 chr12 ... While BED and GENOME ...
bedtools_intersect written 5 days ago by victoria_aleks0
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comparing transcriptomes of two species
... Hello! :) I have an idea of comparing two related but different species in order to learn if there are differences in their expression profiles. I used the bam files after tophat2 mapping in HTSeq to generate "counts-tables" and then chose top most expressed genes and compare the data. My question w ...
transcriptom written 9 months ago by victoria_aleks0 • updated 9 months ago by genomax226k

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