User: emre.cto

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Posts by emre.cto

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Comment: C: Aligned BAM file to gene-cell expression matrix for scRNA-seq
... You can use featurecounts directly on the BAM file which is what the tutorial is doing. Then you can use umi-tools to count the output to generate the gene-cell expression matrix -if your data has UMIs-. ...
written 3 months ago by emre.cto0
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Comment: C: MACS2 --nolambda fold enrichment cutoff
... Thanks, but I didn't understand your argument about single-cell ATAC-seq. The coverage per cell or per cluster can be low but peak calling is done using all reads which treats the sample like bulk. Then the reads are counted per peak per cell. So there is no reason why `--nolambda` shouldn't produce ...
written 4 months ago by emre.cto0
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Comment: C: MACS2 --nolambda fold enrichment cutoff
... After trying both with `--nolambda` and default, I agree with you that there are many false positive looking peaks. I forgot where I saw the suggestion first but many papers use this option. Including the paper for HMMRATAC program written by the same group who developed MACS (they compare with MACS ...
written 4 months ago by emre.cto0
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MACS2 --nolambda fold enrichment cutoff
... In the output file of MACS2, the fold enrichment normally refers to enrichment of summit to local lambda model. I am using `--nolambda` option for ATAC-seq analysis (recommended as there is no input file like Chip-seq). Is the output file now showing enrichment with respect to global lambda? If so, ...
macs2 atac-seq written 4 months ago by emre.cto0 • updated 4 months ago by ATpoint36k
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Comment: C: Remote blast of SRA database
... This solved my problem, thanks! ...
written 5 months ago by emre.cto0
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Remote blast of SRA database
... I am trying to use blast remotely using command line. I want to specify a certain database to blast, and I figured it out for WGS databases: ./blastn -db WGS_VDB://EXAMPLEID01 -query tmp.fa -out out.txt -remote However, I don't know how to do it for SRA databases. Since it is possible to do it ...
sra blast written 5 months ago by emre.cto0 • updated 5 months ago by Brice Sarver3.5k
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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 months 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 months 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 2.1 years 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 2.1 years ago by emre.cto0

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