User: Richard

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Richard550
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550
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Location:
Canada
Last seen:
17 hours ago
Joined:
6 years, 4 months ago
Email:
r****************@gmail.com

Posts by Richard

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merge aligned read pairs that overlap - keep the bases that match the reference
... Hi all, I have aligned paired-end genome data that was sequenced with 150bp reads. The average insert size is just 200bp so there are lots of read pairs with significant overlap of their alignments. I see that there are lots of tools for merging fastq data and at least one that clips overlapping ...
illumina paired-end written 4 weeks ago by Richard550
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miRNA with UMI - any papers showing this improves accuracy?
... Hi Folks, It makes sens to me that using UMIs in miRNA-Seq would allow a user to get more accurate estimates of miRNA expression given how the inserts are really short and PCR is involved. Although I'm finding a number of software packages supporting the analysis of data containing UMI, I'm not fi ...
umi mirna written 6 weeks ago by Richard550 • updated 25 days ago by Biostar ♦♦ 20
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compare SV results across samples - Manta, Delly
... Hi folks, I have Delly and Manta results for a cohort of WGS tumour libraries. Some of the libraries are derived from the same sources using different methods in the lab and I want to be able to compare/contrast the sets of SV calls generated by the tools. Is there any magic sauce out there that ...
wgs manta delly illumina written 10 weeks ago by Richard550 • updated 10 weeks ago by d-cameron1.8k
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Comment: C: merge Bed entries with both ends within maximum distance
... Hi Alex, Thanks for your continued help with this! I have bed elements representing all sort of anomalous read pairs from all around the genome. I am looking to merge (and count) the entries that redundantly represent the same event. To qualify as a matching event I wanted to apply a distan ...
written 3 months ago by Richard550
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Comment: C: merge Bed entries with both ends within maximum distance
... Hi Alex, I was just trying this out, and I'm not quite where I need to be. Can you take a look? Example bed file (output of sort-bed): 9 90917053 90918018 9 90921192 90922024 9 90945236 90946137 9 90982846 90983792 9 91000814 112010931 9 91005014 91005862 9 91009275 9 ...
written 3 months ago by Richard550
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Comment: C: merge Bed entries with both ends within maximum distance
... Hi Devon, I'm trying to merge read pair information that represent anomolous SVs. Given that the length of the SV can be up to a chromosome length, the usual parameters for these tools don't provide options that would suitably merge bed entries that represent the same event, while allowing for the ...
written 3 months ago by Richard550
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Comment: C: merge Bed entries with both ends within maximum distance
... Hi Pierre, I've adjusted my description to be more specific. The Bedtools option is much more lenient than what I am looking for. ...
written 3 months ago by Richard550
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merge Bed entries with both ends within maximum distance
... Hi folks, I have a bed file like the following: 19 52175458 52177604 13 19 52175458 52177663 17 19 52175458 52177717 39 19 52175458 52178717 43 and I would like to be able to merge any entries that have bo ...
next-gen alignment written 3 months ago by Richard550 • updated 3 months ago by Alex Reynolds24k
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extract reads from BAM whose fragments overlap a specified region
... Hi all, What method do you recommend for extracting from a BAM file all the fragments whose insert overlaps a desired coordinate range? Using samtools/sambamba view I can easily extract all the sequenced reads that overlap a region. I'm looking for a command that will do the same, but also repor ...
alignment written 3 months ago by Richard550 • updated 3 months ago by Pierre Lindenbaum110k
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estimate error profile from aligned Illumina reads
... Hi folks, Can anyone recommend a tool that can loop through a BAM file and give me information about which base substitutions are present at each position in the reads? Ideally, it would report a table that would give the estimate error rate at each read position. ...
illumina error_rate written 6 months ago by Richard550 • updated 6 months ago by michael.ante2.5k

Latest awards to Richard

Popular Question 9 weeks ago, created a question with more than 1,000 views. For variant calling on amplicon data
Popular Question 3 months ago, created a question with more than 1,000 views. For variant calling on amplicon data
Popular Question 4 months ago, created a question with more than 1,000 views. For variant calling on amplicon data
Appreciated 6 months ago, created a post with more than 5 votes. For A: Need Recommendations For Aligning Longer (2X250Bp) Reads
Popular Question 6 months ago, created a question with more than 1,000 views. For variant calling on amplicon data
Popular Question 6 months ago, created a question with more than 1,000 views. For Need Recommendations For Aligning Longer (2X250Bp) Reads
Popular Question 6 months ago, created a question with more than 1,000 views. For Fasta Output Python Parsing
Popular Question 6 months ago, created a question with more than 1,000 views. For Mate Pair Alignment Summary
Popular Question 6 months ago, created a question with more than 1,000 views. For Biopython Examples For Writing Genbank Files?
Popular Question 17 months ago, created a question with more than 1,000 views. For variant calling on amplicon data
Appreciated 17 months ago, created a post with more than 5 votes. For A: Need Recommendations For Aligning Longer (2X250Bp) Reads
Popular Question 17 months ago, created a question with more than 1,000 views. For Mate Pair Alignment Summary
Popular Question 17 months ago, created a question with more than 1,000 views. For Need Recommendations For Aligning Longer (2X250Bp) Reads
Popular Question 17 months ago, created a question with more than 1,000 views. For Fasta Output Python Parsing
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Blast Indel Calibration
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Coverage In Bam Alignment
Great Question 19 months ago, created a question with more than 5,000 views. For Tophat-Fusion-Post Error
Popular Question 19 months ago, created a question with more than 1,000 views. For Fasta Output Python Parsing
Popular Question 20 months ago, created a question with more than 1,000 views. For Fasta Output Python Parsing
Popular Question 20 months ago, created a question with more than 1,000 views. For Mate Pair Alignment Summary
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Mate Pair Alignment Summary
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Need Recommendations For Aligning Longer (2X250Bp) Reads
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Biopython Examples For Writing Genbank Files?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Blast Indel Calibration
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Strelka Indel Allele Counts

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