User: newbinf

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newbinf0
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Posts by newbinf

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Comment: C: split BAM file with same cell-barcode and UMI pair
... Sorry for the late reply! I am using the 10x cell barcode tags, they are now placed in the read headers. I cut out the tags because I do not want misalignments caused by the cell barcode and UMI tags. ...
written 12 months ago by newbinf0
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Comment: C: split BAM file with same cell-barcode and UMI pair
... There are only about 50 cell barcodes in my gene/region of interest. So it would be about 50-70 files. I should clarify I used samtools to only grab the portion of the bam file with alignments to one gene. ...
written 12 months ago by newbinf0
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split BAM file with same cell-barcode and UMI pair
... I have single cell RNA-seq reads (from 10x Chromium) that have already been pre-processed. The cell-bacode and UMI tag were cut-and-pasted to the header (via umi-tools) and low quality reads were removed. Next, I mapped the reads (with STAR) and isolated the reads from a gene of interest (via samtoo ...
unique molecular identifier rna-seq umi-tools written 12 months ago by newbinf0
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How to extract reads passing a threshold for Mean Sequence Quality
... I have some RNA-seq data that I trimmed and then ran through FastQC to check the quality. For the R2 file for my read, there seems to be a bad quality score for a large portion of the reads. A lot of the reads are in the red zone. ![This shows that the overall quality of the R2 reads are relative ...
rna-seq written 13 months ago by newbinf0 • updated 13 months ago by genomax74k
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Comment: C: How to move UMI tags to the header
... After skimming through the documentation, this looks like what I need. Thank you! ...
written 14 months ago by newbinf0
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How to move UMI tags to the header
... I have complete sequences from 10x Chromium that look like the following: |----my 16 bp cell barcode----|---8bp 10x UMI---|--SO--|-------------------cDNA (100 bp)----------------------| SO = switch oligo The reads are demultiplexed and don't have the Illumina barcodes in the sequence. I want to ma ...
umi alignment rna-seq written 14 months ago by newbinf0
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Amplicon Based Data
... Hi all, I have amplicon-based data where the reads look like this: forward-adapter + 4bp molecular tag + ligation arm (18-24bp) + sequence of interest + extension arm (18-24 bp) + 4bp molecular tag + reverse-adapter I have both forward and reverse reads (R1 and R2) and they are pair-ended. How do ...
sequencing written 15 months ago by newbinf0
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Answer: A: Understanding Annovar Output
... I realize that DP:RD:AD is total reads: reference allele reads: alternative allele reads. Please correct me if I am wrong. How do I isolate these values. Or are there columns in the VCF file output that contain these values already? ...
written 16 months ago by newbinf0
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Understanding Annovar Output
... I have a vcf output from Annovar (and wAnnovar), and need some help understanding all of the headers. I know i am given the reference and the alternative allele. However, I want to know how many reads in my input file were reference and alternative. I'm looking at the vcf file, and see some traili ...
vcf annovar written 16 months ago by newbinf0 • updated 16 months ago by h.mon28k
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Comment: C: Removing Duplicates before aligning
... I want to delete reads with the exact same sequences (including barcodes) so that I can eliminate any PCR duplicates. I want to make sure that my future variant analysis is not biased because of PCR duplicates. ...
written 16 months ago by newbinf0

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