User: Anjan

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Anjan810
Reputation:
810
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Trusted
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United States
Last seen:
5 months, 2 weeks ago
Joined:
8 years, 5 months ago
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Posts by Anjan

<prev • 31 results • page 1 of 4 • next >
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Comment: C: Which Are The Best Programming Languages For A Bioinformatician?
... In Perl's defence its regular expression capabilities are unmatched by even Python. ...
written 5.5 years ago by Anjan810
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6
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Comment: C: Downloading And Maintaining A Local, Blast-Able Nr Database
... AFAIK, NCBI does a weekly release of data every Monday. HTH. ...
written 5.6 years ago by Anjan810
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Comment: C: Remove Duplicates Workflow
... @Dan. Yes, it is indeed amplicon based. We design primers to amplify specific regions in our genome of interest. These are then fragmented and used in the library prep process. Do you have any references for "recommendations not to dedup data when doing amplicon-based sequencing"? Many thanks. ...
written 5.6 years ago by Anjan810
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Comment: C: Remove Duplicates Workflow
... @Razzmataz- this is a targeted sequencing panel, we do expect to see high coverage in a relatively small region. ...
written 5.6 years ago by Anjan810
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5 follow
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Remove Duplicates Workflow
... Hello all, Am using samtools to remove duplicates. Here is my workflow for removing duplicates from a *.bam file. 1. Sort bam file by readname. 2. Run the fixmate command on the sorted file. This apparantly fills in mate coordinates, ISIZE and mate-related flags into the output .bam file. 3. Sort ...
ngs samtools written 5.6 years ago by Anjan810 • updated 5.6 years ago by Alastair Kerr5.2k
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Comment: C: Ngs - Huge (Fastq) File Parsing - Which Language For Good Efficiency ?
... No Perl? The workhorse of most bioinformaticians around the world. Please see comments on Perl being >10X faster than Python in regex parsing. ...
written 5.7 years ago by Anjan810
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Why Is A Base Quality Score Associated With A Base Deletion In A Pileup File?
... Hi, It turns out that a pileup generated from a .bam file, by samtools (option mpileup), assigns a base quality score to a base deletion. In the example below there is a G deleted from position 53 in a read aligning to the phiX sequence. This is indicated by a "" in the pileup at line 53. This "" ...
next-gen samtools written 6.6 years ago by Anjan810 • updated 6.5 years ago by fo3c430
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How Are Sequencing Error Rates Defined?
... Frequently one hears about Illumina's error rate being 0.8% or thereabouts. How is this error rate calculated? A few possibilities come to mind: total number of incorrect bases sequenced as a percentage of total number of sequenced bases. expected percentage of incorrect bases in any given positio ...
next-gen error written 6.6 years ago by Anjan810 • updated 6.6 years ago by Chris Miller21k
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Comment: C: Depth Of Coverage Reported By Igv And Samtools Do Not Agree
... Sean, Thanks for the feed back. Indeed I am using the default filter in the mpileup command to get rid of low quality bases. However I am looking for documentation for your second assertion that "mpileup" also removes duplicates. The samtools manual does not explictly state this. Thanks again. Anja ...
written 6.6 years ago by Anjan810
35
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4
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19 follow
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Depth Of Coverage Reported By Igv And Samtools Do Not Agree
... Hi all, I have several samples that have been sequenced on a MiSeq platform using a paired end protocol. Each read set of each sample was individually aligned using BWA (to the relevant reference sequence). Paired read sets were merged using samtools (option sampe) to produce the .sam files. The .s ...
next-gen samtools igv written 6.6 years ago by Anjan810 • updated 4.6 years ago by -_-830

Latest awards to Anjan

Good Question 9 months ago, asked a question that was upvoted at least 5 times. For How Does A Bioinformatics Scientist Document His/Her Work?
Appreciated 14 months ago, created a post with more than 5 votes. For C: Which Are The Best Programming Languages For A Bioinformatician?
Epic Question 19 months ago, created a question with more than 10,000 views. For How Does A Bioinformatics Scientist Document His/Her Work?
Appreciated 2.4 years ago, created a post with more than 5 votes. For C: Which Are The Best Programming Languages For A Bioinformatician?
Great Question 2.4 years ago, created a question with more than 5,000 views. For Bwa Aln And Samse Options
Popular Question 2.8 years ago, created a question with more than 1,000 views. For How Are Sequencing Error Rates Defined?
Great Question 3.4 years ago, created a question with more than 5,000 views. For Depth Of Coverage Reported By Igv And Samtools Do Not Agree
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Automatic Clustering Of Biological Sequences
Commentator 3.6 years ago, created a comment with at least 3 up-votes. For C: Which Are The Best Programming Languages For A Bioinformatician?
Student 3.9 years ago, asked a question with at least 3 up-votes. For Depth Of Coverage Reported By Igv And Samtools Do Not Agree
Great Question 4.0 years ago, created a question with more than 5,000 views. For How Does A Bioinformatics Scientist Document His/Her Work?
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Automatic Clustering Of Biological Sequences
Epic Question 4.2 years ago, created a question with more than 10,000 views. For Downloading And Maintaining A Local, Blast-Able Nr Database
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Consensus Quality And Snp Quality In Samtools
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Running Blast On Amazon'S Elastic Mapreduce
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Bwa Aln And Samse Options
Appreciated 5.3 years ago, created a post with more than 5 votes. For Downloading And Maintaining A Local, Blast-Able Nr Database
Great Question 5.3 years ago, created a question with more than 5,000 views. For Downloading And Maintaining A Local, Blast-Able Nr Database
Good Question 5.3 years ago, asked a question that was upvoted at least 5 times. For Downloading And Maintaining A Local, Blast-Able Nr Database
Popular Question 5.3 years ago, created a question with more than 1,000 views. For Problem Installing Velvet Assembler On Mac Os X 10.5.8
Popular Question 5.3 years ago, created a question with more than 1,000 views. For Running Blast On Amazon'S Elastic Mapreduce
Popular Question 5.3 years ago, created a question with more than 1,000 views. For Bwa Aln And Samse Options
Popular Question 5.3 years ago, created a question with more than 1,000 views. For Downloading And Maintaining A Local, Blast-Able Nr Database
Popular Question 5.4 years ago, created a question with more than 1,000 views. For Downloading And Maintaining A Local, Blast-Able Nr Database
Appreciated 7.2 years ago, created a post with more than 5 votes. For How Does A Bioinformatics Scientist Document His/Her Work?

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