User: tim.ivanov.92

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Posts by tim.ivanov.92

<prev • 42 results • page 1 of 5 • next >
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Comment: C: Get gene counts from *.sam file and annotation
... thats not really solving my problem, i first need to use something like bedtools intersect ...
written 9 days ago by tim.ivanov.920
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Comment: C: Get gene counts from *.sam file and annotation
... yeah, thats what my goal is the beast i've found so far is bedtools intersect ...
written 9 days ago by tim.ivanov.920
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Get gene counts from *.sam file and annotation
... I have a list of alignment (*.sam/*.bam formats) from RNAseq experiment and i want to get gene counts from them. The problem is that these alignments have chromosomes as reference, not genes: NB501288_407_HGYJKBGX7:1:11101:22149:1027#GAGATTGTCAGT 0 chr8 141541926 37 70M ...
alignment samtools rna-seq written 10 days ago by tim.ivanov.920
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Comment: C: *.sra files info
... ok, thank you for the answer, then i'll just align them all ...
written 14 days ago by tim.ivanov.920
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Comment: C: *.sra files info
... What is the content of the archive: is it unmapped reads (which i will need to align then) or is it already aligned *.sam file ...
written 15 days ago by tim.ivanov.920
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*.sra files info
... I've downloaded a lot of *sra archives, and i want to get information about the content of each of them. Can i do it without extracting every archive? ...
next-gen sra toolkit written 15 days ago by tim.ivanov.920
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Comment: C: Can i use ucsc track browser without a reference organism?
... thank you for your reply, but it looks like IBS is only a manual draw tool - which is not uncomfortable for drawing ~ 50 organisms, each having ~ 20 features from that list - i've seen a few, but none of them seems to have an option of importing users features Can you point me on a tool that can, i ...
written 25 days ago by tim.ivanov.920
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Comment: C: Can i use ucsc track browser without a reference organism?
... Thank you for your links - i'll definitely look into it! My features are two lists of exons - one from annotation, and one from my predictions. I want to see their intersection and visualize them ...
written 27 days ago by tim.ivanov.920
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Comment: C: Strand not working in biopython efetch
... No i can't! Thank you - that did it, i was using `1`, `-1` instead ...
written 28 days ago by tim.ivanov.920
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Can i use ucsc track browser without a reference organism?
... Can i access ucsc *.BED track visualization instrumental for my own alignment file? This is very weird question, but i can't find any tool, for adding tracks on multiple alignment file. I have a standard clustalw alignment file for ~21 organism. And each of these organism has some features, which i ...
aln annotation clustalw ucsc written 28 days ago by tim.ivanov.920

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