Forum: Bioinformatics
04-26-2019, 02:47 PM
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Replies: 1
Views: 1,128
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Forum: Bioinformatics
03-21-2019, 01:04 PM
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Replies: 0
Views: 731
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Forum: De novo discovery
03-20-2019, 11:25 AM
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Replies: 1
Views: 3,619
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Forum: Bioinformatics
03-17-2019, 07:41 PM
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Replies: 678
Views: 212,346
How do I run the basic BBmap.sh script in...
How do I run the basic BBmap.sh script in Windows? What is the corresponding java command? I want to align four sets of paired-end Illumina RNA-Seq reads to a genome assembly. I am particularly...
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Forum: RNA Sequencing
03-04-2019, 03:25 PM
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Replies: 1
Views: 1,498
visualizing RNAseq mapping to reference
I'm using Geneious (for Windows), which has two RNA Seq mappers (Geneious RNA Mapper, and BBmap). I'm looking for introns in a set of individual gene sequences. Mapping results in Geneious are...
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Forum: General
08-25-2016, 08:33 AM
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Replies: 6
Views: 3,615
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Forum: Illumina/Solexa
12-06-2014, 07:38 AM
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Replies: 35
Views: 15,263
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Forum: Illumina/Solexa
12-03-2014, 08:52 AM
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Replies: 35
Views: 15,263
I don't know; the second variant seems to be...
I don't know; the second variant seems to be saying to me , 'the reads from the right side of the library read (post-linker, 454_2.fastq) belong at the right end of the genome fragment' -- which...
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Forum: Illumina/Solexa
12-02-2014, 06:43 PM
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Replies: 35
Views: 15,263
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Forum: Illumina/Solexa
12-01-2014, 03:38 PM
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Replies: 35
Views: 15,263
But 454 paired end reads are two 'end' reads...
But 454 paired end reads are two 'end' reads connected by a linker sequence. Does the IonHammer corrector actually recognize those and split the reads before correcting? Or do the 454 PE reads...
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Forum: Illumina/Solexa
12-01-2014, 10:54 AM
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Replies: 35
Views: 15,263
re: attempting SPAdes with 454 reads -- if I...
re: attempting SPAdes with 454 reads -- if I understand correctly:
2) SPAdes does not natively support 454 reads
2) 454 reads resemble Ion Torrent reads (similar technology) but SPAdes will...
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Forum: De novo discovery
11-21-2014, 10:20 AM
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Replies: 8
Views: 3,012
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Forum: De novo discovery
11-19-2014, 03:31 PM
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Replies: 8
Views: 3,012
The example in the mulitple platform manifest...
The example in the mulitple platform manifest *seems* to indicate the 454 PEs can be left as one fastq file. The insert size and SD need to be provided (which I can do) or 'autorefine' to let MIRA...
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Forum: De novo discovery
11-19-2014, 02:38 PM
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Replies: 8
Views: 3,012
That helps a lot (for MIRA) , thanks!
So as...
That helps a lot (for MIRA) , thanks!
So as long as I convert the 454 Paired End sff to Fastq with sff_extract, MIRA will process and assemble them correctly *as paired ends*? It still...
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Forum: De novo discovery
11-19-2014, 12:19 PM
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Replies: 8
Views: 3,012
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Forum: Illumina/Solexa
11-18-2014, 01:47 PM
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Replies: 145
Views: 321,421
Illumina helped sort me out. The seqs I posted...
Illumina helped sort me out. The seqs I posted last time are from an old , discontinued version of the kit (pp 20-21 of the July 2014 letter). The newer TruSeq adapters('universal' and 'indexed')...
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Forum: Illumina/Solexa
11-17-2014, 07:18 PM
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Replies: 145
Views: 321,421
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Forum: Bioinformatics
11-07-2014, 10:54 AM
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Replies: 11
Views: 5,345
I'm trying (on Windows 7) to use Next...
I'm trying (on Windows 7) to use Next Workbench 3's SFF editor on some 454 sff files, but when I do end clipping and filtering, none of it is saved and the sequence itself never changes even...
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Forum: Bioinformatics
10-06-2014, 02:26 PM
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Replies: 14
Views: 4,685
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Forum: Bioinformatics
10-02-2014, 02:18 PM
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Replies: 14
Views: 4,143
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Forum: Bioinformatics
10-01-2014, 12:17 PM
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Replies: 14
Views: 4,143
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Forum: Bioinformatics
09-30-2014, 02:35 PM
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Replies: 14
Views: 4,143
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Forum: Bioinformatics
09-30-2014, 10:08 AM
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Replies: 14
Views: 4,143
tried it but 'java' was not recognized as a...
tried it but 'java' was not recognized as a command. I added the path to 'my' java.exe
and reran, but then it threw this error
Error: Could not find or load main class jgi.ReformatReads
...
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Forum: Bioinformatics
09-29-2014, 05:49 PM
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Replies: 14
Views: 4,143
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Forum: Bioinformatics
09-29-2014, 10:05 AM
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Replies: 2
Views: 2,187
the introduction of this pape...
the introduction of this pape (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4027187/)r contains nice brief descriptions of many of the softwares used to find and analyse genomic repeats.
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