User: sullis02

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sullis020
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Posts by sullis02

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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 2 days ago by sullis020
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Comment: C: working with Sanger fasta + qual + clip files
... Thank you very much!! ...
written 3 days 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 7 days 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 7 days 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 8 days 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 8 days 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 8 days 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 9 days 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 10 days ago by sullis020
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working with Sanger fasta + qual + clip files
... I have an old Sanger fasta file and its associated qual file, as well as a 'clip' file that shows where to trim low-quality sequence for each fasta sequence. e.g. for the first record in the fasta file here are the corresponding data in each file: fasta: >gnl|ti|713904976 1047095293492 ...
sanger trimming fastq written 5 weeks ago by sullis020 • updated 5 weeks ago by JC7.7k

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