User: sullis02

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sullis020
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Posts by sullis02

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Comment: C: Misunderstood parameter of NCBI BLAST
... Which is actually properly cited in the Shah et al. paper: "This functionality was first reported as a bug to NCBI by Kumar (2015), and later documented in a blog post (Cock, 2015) by Peter Cock." ...
written 14 days ago by sullis020
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Comment: C: working with Sanger fasta + qual + clip files
... Oops, wrote to soon. Have you tried your script with input files that contain more than a single fasta/clip/qual record? With a single record as input (as in your example) it works fine. With normal fasta /qual/clip files (which contain numerous records) it doesn't work it reports ' clip id does ...
written 3 months ago by sullis020
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Comment: C: working with Sanger fasta + qual + clip files
... Thank you very much!! ...
written 3 months ago by sullis020
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Comment: C: adding pair info to fastq files, for BWA
... NB that even if bwa index chose the wrong -a option, bwa mem will still output a .sam file. So it's worth checking. ...
written 4 months ago by sullis020
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Comment: C: adding pair info to fastq files, for BWA
... Problem solved. It was due to incorrect bwa indexing. By default (I use v 0.7.17, though 0.7.15 exhibited the same behavior), the bwa index -a option is set to 'auto', which means bwa index itself decides whether to use the 'bwtsw' (large reference sequence) or 'is' (small) setting (or 'rb2' but I ...
written 4 months ago by sullis020
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Comment: C: adding pair info to fastq files, for BWA
... Sorry, my reply should have gone here. Instead it's following my first post up there. ...
written 4 months ago by sullis020
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Comment: A: adding pair info to fastq files, for BWA
... I also tried a completely different pair of fastq files, generated by our sequencing core (not downloaded), with headers like this R1.fastq @HWI-ST911:230:C4MVUACXX:2:1101:1483:2058 1:N:0:ACAGTG R2.fastq @HWI-ST911:230:C4MVUACXX:2:1101:1483:2058 2:N:0:ACAGTG run: [M::bw ...
written 4 months ago by sullis020
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Comment: A: adding pair info to fastq files, for BWA
... I've tried (almost) everything you suggested (I reduced the fastq sizes down to 20000 lines, i.e., just the first 5000 fastq records, just to make testing faster). Nothing was recognized as FR. Here for example are three different ID header versions of the first record. The first one is the heade ...
written 4 months ago by sullis020
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adding pair info to fastq files, for BWA
... I downloaded a file of Illumina paired reads from SRA. When split into _1 and _2 using the sratools fastq_dump --split-files, the fastq record IDs looks like this (I'm showing just the identifier lines of the first record in each file) _1.fastq @SRR4734558.1 HWI-ST1117:138:C1HR1AC ...
illumina bwa sra written 4 months ago by sullis020
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Comment: A: Racon-Illumina or Pilon?
... ? It looks here like 3a is the best result, and that's the one with no polishing. ...
written 4 months ago by sullis020

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