User: bertb

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bertb10
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Posts by bertb

<prev • 29 results • page 1 of 3 • next >
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bam_stat.py and featureCounts stats don't seem to make sense (to me)
... Hello, Tl;dr - can low quality (non-unique) alignments (according to bam_stat.py) be considered multimappers by featureCounts? I have an RNAseq bam file (subsetted for troubleshooting) that when I run featureCounts, it tells me I have multimapping reads. However, this bam file has been filtered fo ...
alignment rna-seq written 6 days ago by bertb10
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Comment: C: How to filter out chromosome regions from a .bam file
... This worked well. Thank you! ...
written 6 days ago by bertb10
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How to filter out chromosome regions from a .bam file
... Hello, I know that I can create a subset of a bam file for a desired region using `samtools view`: samtools view -b UWNsub100k_int.bam chrXII:450000-470000 > UWNsub100k_ribos.bam What I want to do, however, is create a .bam file that *excludes* these regions. Perhaps something similar to ...
alignment rna-seq written 10 days ago by bertb10 • updated 10 days ago by John Marshall2.1k
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How to unique mappers become concordant pairs aligned >1 times
... Hello, I prepared .sam files from PE sequencing results as follows: hisat2 -p 8 --rg-id=UWN_t3 --rg SM:UWN_t3 --rg LB:UWN_t3 --rg PL:ILLUMINA --rg PU:CE9PNANXX.8 -x $RNA_REF_INDEX --dta --rna-strandness RF -1 $RNA_DATA_DIR/trimmed/UW_N_Mix.trimmed_1.fastq.gz -2 $RNA_DATA_DIR/trimmed/UW_N_Mix.t ...
alignment rna-seq written 18 days ago by bertb10
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Comment: C: how to identify where multi-mappers, or "non primary hits" are mapping to
... Ok. That's a lot of helpful information. Thanks again ...
written 24 days ago by bertb10
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Comment: C: how to identify where multi-mappers, or "non primary hits" are mapping to
... Ok, good to know. Thanks for your response. 2 quick points that maybe you can help with: 1. When I ran featureCounts with option -M to include multimappers in the count (see above for code & output), it got rid of all the multimappers category, but instead of assigning them to multiple genes, as ...
written 26 days ago by bertb10
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Comment: C: how to identify where multi-mappers, or "non primary hits" are mapping to
... Thanks for your reply. I apologize if I sound like I keep repeating myself, but is there any way to identify the multiple locations that the reads are trying to assign to? ...
written 4 weeks ago by bertb10
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Comment: C: how to identify where multi-mappers, or "non primary hits" are mapping to
... Thank you for your response. The command I used for alignment was: hisat2 -p 8 --rg-id=UWN_t2 --rg SM:UWN_t2 --rg LB:UWN_t2 --rg PL:ILLUMINA --rg PU:CW9PNANXS.8 -x $RNA_REF_INDEX --dta --rna-strandness RF -1 $RNA_DATA_DIR/R1.fastq.gz -2 $RNA_DATA_DIR/R2.fastq.gz -S ./UWN_t2.sam I understand t ...
written 4 weeks ago by bertb10
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how to identify where multi-mappers, or "non primary hits" are mapping to
... Hello, My RNAseq alignment QC is showing me that I have a fair number of "non primary hits", which, as I understand it, means the read has been mapped to multiple locations. (I created a very small subsample file of my .bam file in order to try and find where these reads are mapping.): bam_sta ...
alignment next-gen rna-seq written 4 weeks ago by bertb10
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Comment: C: featureCount with high multimapping fragments
... Thanks for your help. Can you tell me how I can parse which reads are aligning or mapping to multiple places? From what I've read there are NH tags in the .bam files, but I'm not sure how I can separate these, or see which features they are mapping to. Thanks ...
written 4 weeks ago by bertb10

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Popular Question 23 months ago, created a question with more than 1,000 views. For MACS2 won't build model - too few paired peaks, but I'm not using paired data

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