User: jingtao09

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jingtao09110
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Posts by jingtao09

<prev • 19 results • page 1 of 2 • next >
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Tool: Deindexer - A Standalone Demultiplexing Tool For Illumina Platform
... deindexer A Standalone Demultiplexing Tool for Illumina Platform Features No need to edit SampleSheet.csv files Support your own barcode library Support many mismatches on barcode[s] (Currently Illumina only allows 1 mismatch) Easy to use: support single barcode to dual barcode or multiple ba ...
illumina tool written 6.7 years ago by jingtao09110
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Comment: C: Identifying Bacteria Species In Metagenomics
... if you using Genomic NGS data, then you loss the sensitivities. You could mapping all of the NGS reads - with all possible hits ,then classify them by Genus -> Species. After the couple reduction and summarization, then you would have your answer what is in there Species Wise. Now, it is time y ...
written 7.2 years ago by jingtao09110
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Comment: C: Blast2Go Pipeline
... blast2go has pie chart ...
written 7.3 years ago by jingtao09110
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Comment: C: Convert Bowtie Output To Bwa
... Z: means the value follows are strings. by look at the definition of XA - chr,pos,CIGAR,NM; I think you can do this, // keep the last line parsed in record and compare to the current parsed line. vector=empty lastline=getline() while current=getline(): if the current is same as la ...
written 7.3 years ago by jingtao09110
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Comment: C: Convert Bowtie Output To Bwa
... https://github.com/lh3/bwa/blob/master/xa2multi.pl is this waht you want? it expands the xa from bwa sam files. ...
written 7.3 years ago by jingtao09110
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Comment: C: Bwa - How To Use Xm Tag
... you cannot extract from sai file, but the final sam file. ...
written 7.3 years ago by jingtao09110
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Comment: C: Bwa - How To Use Xm Tag
... so you can do one time bwa -n4, then you can subtract all n=0,1,2,3 reads. No easy way to compare to bowtie with the edit distance definitions. Cause bwa using Smith-Waterman algo, which assign different compensations to sub and indels. The best you cand do is to retrieve the alignment and calculat ...
written 7.3 years ago by jingtao09110
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Comment: C: Best Practice On Variant Discovery For Bacteria?
... BWA/MAQ for sure. all the other aligner/mapper are having some sort of dishonest to the truth.(Sorry to say that, but that is what I found after my in house test). Even though, in some specical cases, bwa still has incorrect mappings. But it is the best in current(speed, space, and correctness) sin ...
written 7.3 years ago by jingtao09110
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Comment: C: Bwa - How To Use Xm Tag
... you need combine XM and NM tags together. And also it depends on what is your definitions on mismatches. If sub, indels are all included, then bwa wont give the number directly out of your screen. Recovery the alignment with CIGAR ,read and reference would be the most correct way but time consuming. ...
written 7.3 years ago by jingtao09110
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Comment: C: Suggested Options For Casava 1.8 (Bcl > Fastq)
... here is the info from CASAVA1.8.2 (I highly recommend you to upgrade to 1.8.2) 1 Enter: /path-to-CASAVA/bin/configureBclToFastq.pl --input-dir <BaseCalls_dir> --output-dir <Unaligned> --sample-sheet <input_dir>/SampleSheet.csv 2 Go to the <Unaligned> folder. 3 Ru ...
written 7.3 years ago by jingtao09110

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