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Search: Posts Made By: ssully
Forum: General 08-25-2016, 08:33 AM
Replies: 6
Views: 2,014
Posted By ssully
You are getting the 10 best target sequences for...

You are getting the 10 best target sequences for each query. For some of the queries, there is more than one hit (hsp) to the target. Those are returned too, so sometimes there are more than 10...
Forum: Illumina/Solexa 12-06-2014, 07:38 AM
Replies: 35
Views: 12,904
Posted By ssully
I worked out the correct orientation and order of...

I worked out the correct orientation and order of 454 paired reads input for SPAdes, and have corrected the reads with --iontorrent option (ionhammer). Btu now I have questions regarding ionhammer...
Forum: Illumina/Solexa 12-03-2014, 08:52 AM
Replies: 35
Views: 12,904
Posted By ssully
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...
Forum: Illumina/Solexa 12-02-2014, 06:43 PM
Replies: 35
Views: 12,904
Posted By ssully
I have removed the linkers and split the 454 mate...

I have removed the linkers and split the 454 mate pair reads with sff_extract; I have them now as (after deinterlacing) a pair of fastq files (454_1.fastq and 454_2.fastq) containing reads _1 and...
Forum: Illumina/Solexa 12-01-2014, 03:38 PM
Replies: 35
Views: 12,904
Posted By ssully
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...
Forum: Illumina/Solexa 12-01-2014, 10:54 AM
Replies: 35
Views: 12,904
Posted By ssully
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...
Forum: De novo discovery 11-21-2014, 10:20 AM
Replies: 8
Views: 2,379
Posted By ssully
That was the wrong way to do it -- instead I've...

That was the wrong way to do it -- instead I've joined the MIRA user forum, which is what the author recommends.
Forum: De novo discovery 11-19-2014, 03:31 PM
Replies: 8
Views: 2,379
Posted By ssully
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...
Forum: De novo discovery 11-19-2014, 02:38 PM
Replies: 8
Views: 2,379
Posted By ssully
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...
Forum: De novo discovery 11-19-2014, 12:19 PM
Replies: 8
Views: 2,379
Posted By ssully
de novo assembly including Illumina and 454 paired-end reads

There's a bunch of hybrid de novo assembly threads but not sure I'm finding the answers to these questions, specifically about paired-end reads from two platforms (Illumina and 454).

454's 'paired...
Forum: Illumina/Solexa 11-18-2014, 01:47 PM
Replies: 145
Views: 301,578
Posted By ssully
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')...
Forum: Illumina/Solexa 11-17-2014, 07:18 PM
Replies: 145
Views: 301,578
Posted By ssully
I'm quite lost. I've got a set of paired end 100...

I'm quite lost. I've got a set of paired end 100 nt HiSeq reads (library insert size was ~300bp) from a colleague and I can't determine what adapter sequences to trim. The current Illumina letter ...
Forum: Bioinformatics 11-07-2014, 10:54 AM
Replies: 11
Views: 4,176
Posted By ssully
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...
Forum: Bioinformatics 10-06-2014, 02:26 PM
Replies: 14
Views: 3,167
Posted By ssully
mview (http://bio-mview.sourceforge.net/)

mview (http://bio-mview.sourceforge.net/)
Forum: Bioinformatics 10-02-2014, 02:18 PM
Replies: 14
Views: 3,155
Posted By ssully
When I wrote 'I don't have 140 Gb of RAM' I meant...

When I wrote 'I don't have 140 Gb of RAM' I meant on my workstation (it has 32Gb). But I do have access to a cluster where I can allocate >140 gb to a job . Should I try that or are you suggesting...
Forum: Bioinformatics 10-01-2014, 12:17 PM
Replies: 14
Views: 3,155
Posted By ssully
Hmm..the interleaved file is 140 million reads. ...

Hmm..the interleaved file is 140 million reads. I don't have 140 Gb of RAM. Guess I have to run this on a unix cluster. Is the corrected package (for running the dedup command) ready for download?
Forum: Bioinformatics 09-30-2014, 02:35 PM
Replies: 14
Views: 3,155
Posted By ssully
That works! Thanks.

That works! Thanks.
Forum: Bioinformatics 09-30-2014, 10:08 AM
Replies: 14
Views: 3,155
Posted By ssully
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
...
Forum: Bioinformatics 09-29-2014, 05:49 PM
Replies: 14
Views: 3,155
Posted By ssully
I installed BBmap on my Windows 7 machine (Java...

I installed BBmap on my Windows 7 machine (Java RE 1.7 is installed). But I can't seem to get dedup to read any of my input files. They're standard paired fastq files I named test1.f1 and...
Forum: Bioinformatics 09-29-2014, 10:05 AM
Replies: 2
Views: 1,679
Posted By ssully
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.
Forum: Bioinformatics 09-23-2014, 11:32 AM
Replies: 9
Views: 1,999
Posted By ssully
Perhaps if you do one of your own CEGMA runs, try...

Perhaps if you do one of your own CEGMA runs, try checking as I did and see if you get incompletely overlapping results in those two outputs.
Forum: Bioinformatics 09-23-2014, 09:14 AM
Replies: 9
Views: 1,999
Posted By ssully
Sorry, I wasn't really referring to the two /data...

Sorry, I wasn't really referring to the two /data files (kogs.fa and completeness_cutoff.tbl) I was referring to my output files. Let's call them my.completeness_report and my.cegma.fa

we've ...
Forum: Bioinformatics 09-22-2014, 02:53 PM
Replies: 9
Views: 1,999
Posted By ssully
I did remove all the KOG suffixes before pattern...

I did remove all the KOG suffixes before pattern matching. ..so the disparity isn't due to that. It really appears that the .completeness_report KOGs are not fully included within the .fa file KOGS....
Forum: Bioinformatics 09-19-2014, 03:46 PM
Replies: 9
Views: 1,999
Posted By ssully
Thanks for explaining that. I now have my...

Thanks for explaining that. I now have my lookup table.

Another thing I'd like to be clearer on: the relationship between the 'completeness' metrics and the rest of the output. For exmaple:
...
Forum: Bioinformatics 09-16-2014, 09:24 AM
Replies: 9
Views: 1,999
Posted By ssully
CEGMA VM: questions about inputs and outputs

CEGMA VM, by default, uses a 'kogs.fa' file as the protein sequence input to compare to the user's genome sequence input.

kogs.fa contains ~2700 sequences, which I am guessing is the complete...
Showing results 1 to 25 of 43

 


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