User: Nathan S. Watson-Haigh

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Posts by Nathan S. Watson-Haigh

<prev • 14 results • page 1 of 2 • next >
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Answer: A: military application of bioinformatics
... The Australian Department of Defence Science & Technology use bioinformatics in the areas of defence against biological and chemical threats. Perhaps look at publications with this affiliation to get some ideas. https://www.dst.defence.gov.au/capability/chemical-and-biological-defence ...
written 20 months ago by Nathan S. Watson-Haigh190
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Comment: C: loop over lines group by group and do something separately in text file
... Thank's Ole that's great info!! I've updated my answer to use `--remove-rec-sep` instead of the seperate `awk` command. Note, the doc describes `--remove-rec-sep`, `--rrs` and `--removerecsep` but no mention of `--remove-record-separators`. ...
written 4.5 years ago by Nathan S. Watson-Haigh190
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Answer: A: loop over lines group by group and do something separately in text file
... Others have said you can do this with programming logic and Pierre has shown how GNU Parallel could be used to process the blocks. I'd like to expand on the idea of using GNU Parallel to process your blocks and do away with reading/writing the blocks to intermediary files. This way you can process y ...
written 4.5 years ago by Nathan S. Watson-Haigh190
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Calculating Fpkm/Rpkm For Each Read Group Given A Gtf File
... I have a couple of BAM files, each containing several read groups, and an associated GTF file. I'd like to calculate the FPKM/RPKM's for each transcript for each read group. One of the files is from single-end reads, the other from paired-end reads. Is there an existing tool that can calculate the ...
gtf rpkm fpkm rna-seq written 5.2 years ago by Nathan S. Watson-Haigh190
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Samtools Merge/Reheader Of Bam Files With Different @Sq Lines
... I have a bunch of SAM/BAM files which have a different subset of reference sequences missing from the headers (@SQ) lines. samtools merge won't merge them because they have a mismatch in the @SQ lines. I thought specifying -h with a file containing the union of all @SQ lines should work, but it stil ...
ngs samtools written 5.7 years ago by Nathan S. Watson-Haigh190 • updated 2.1 years ago by Biostar ♦♦ 20
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Answer: A: Comparing 2 Large Lists (Millions Of Rows) To Identify Shared And Exclusive Elem
... I find that this blog about performing set operations in the Unix shell to be a great reference: http://www.catonmat.net/blog/set-operations-in-unix-shell-simplified/ It's worth testing different approaches for memory usage and speed. Also if you use a recent version of GNU sort you can specify the ...
written 6.3 years ago by Nathan S. Watson-Haigh190
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Answer: A: Sorting Fastq Files After Trimming (Orphans And Pe)
... I've done something like this previously. I.e. take two fastq files for the /1 and /2 read pairs, do quality trimming etc and then interleave them into a single fastq file and spit out orphans into their own file. My approach (http://bigsa.org.au/node/92) uses cdbfasta and awk: Use cdbfasta to ind ...
written 6.4 years ago by Nathan S. Watson-Haigh190
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Comment: C: Paired-End Sam Flag Mismatch During Filtering
... See SeqAnswers for a thread, dated early 2010, that seems related: http://seqanswers.com/forums/showthread.php?t=5347 In particular, comment #10 provides an example that seems to show similar issues to yours with with the flags. A comment (#13) by Heng states: "Sometimes bwa flags read1 as unmappe ...
written 6.4 years ago by Nathan S. Watson-Haigh190
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Answer: A: Paired-End Sam Flag Mismatch During Filtering
... Considering the circular nature of this reference DNA may be confusing the situation? It appears, to me at least, that the issue is in an incorrect flag for the first read. I would say that the flag of the first alignment (77) is wrong and should be (73) i.e. read is mapped. This is clear from the ...
written 6.4 years ago by Nathan S. Watson-Haigh190
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Comment: C: Paired-End Sam Flag Mismatch During Filtering
... Can you supply an example of the alignment lines, as generated by BWA, of such a pair? ...
written 6.4 years ago by Nathan S. Watson-Haigh190

Latest awards to Nathan S. Watson-Haigh

Appreciated 2.6 years ago, created a post with more than 5 votes. For A: loop over lines group by group and do something separately in text file
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Calculating Fpkm/Rpkm For Each Read Group Given A Gtf File
Good Answer 4.5 years ago, created an answer that was upvoted at least 5 times. For A: loop over lines group by group and do something separately in text file
Appreciated 4.5 years ago, created a post with more than 5 votes. For A: loop over lines group by group and do something separately in text file
Scholar 4.5 years ago, created an answer that has been accepted. For A: loop over lines group by group and do something separately in text file
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Popular Question 5.1 years ago, created a question with more than 1,000 views. For Samtools Merge/Reheader Of Bam Files With Different @Sq Lines
Teacher 6.6 years ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data

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