User: emre.cto

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emre.cto0
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Posts by emre.cto

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Comment: C: Remove duplicate reads in single cell bam file
... Yes it is 10x data and I have multiple cells in a single BAM file. I want to remove the duplicates based on plain sequence, I do not have UMI sequence. ...
written 12 weeks ago by emre.cto0
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Remove duplicate reads in single cell bam file
... Is there a tool to remove duplicated reads from single cell bam file? I am currently dealing with single cell atac-seq file and apparently people have used their own custom scripts for that. E.g this article: [https://www.sciencedirect.com/science/article/pii/S0092867418308559?via][1] [1]: http ...
bam atac seq single cell written 12 weeks ago by emre.cto0
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Answer: A: Collapsing poorly supported nodes into polytomies in R - using 'Phangorn' and 'a
... It has been years since the question was posted but if anyone is still looking for an easy answer, itol allows you to delete the branches under a certain threshold of bootstrap value that you specify. You can extract the resulting tree in any graphical or text format (svg, newick, pdf etc.) https:/ ...
written 16 months ago by emre.cto0
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Comment: C: BLAST+ error: No alias or index file found for nucleotide database
... it should work if you tell blast the full path of the database. you can try the following; tblastn -db /home/cadav/Thesis/VanDePeerPSgenes/Shiu_Pipeline/BLAST_output/Ptr_protDB -query AnchorPoint/AnchorPoint_masked01.fa -out AP01.blasted -evalue 0.0001 -outfmt 7 -matrix BLOSUM50 -lcase_masking ...
written 16 months ago by emre.cto0

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