SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 12 of 12
Search took 0.00 seconds.
Search: Posts Made By: gringer
Forum: Bioinformatics 08-05-2018, 06:32 AM
Replies: 104
Views: 41,706
Posted By gringer
Wow! Joined in 2014, only one post, and you chose...

Wow! Joined in 2014, only one post, and you chose to make your first post something about mutant clouds in response to a 3-year old post of mine from the first page of this thread. I'm not sure if I...
Forum: Bioinformatics 06-30-2016, 03:06 AM
Replies: 104
Views: 41,706
Posted By gringer
From the error messages, your input read files...

From the error messages, your input read files are corrupted:



Do you have any other program that can read the files to check for errors? At the very least, a simple count of lines would be...
Forum: Bioinformatics 10-20-2015, 04:16 PM
Replies: 104
Views: 41,706
Posted By gringer
I've recently discovered that these are...

I've recently discovered that these are transcript sequences, not genomic sequences (despite the initial assurance against that). So the 140,000x coverage and 500x coverage could possibly be for...
Forum: Bioinformatics 10-17-2015, 04:48 AM
Replies: 104
Views: 41,706
Posted By gringer
Increasing k didn't help. If anything, it made...

Increasing k didn't help. If anything, it made the assembly worse. I've been able to generate 110 contigs with a coverage >500 and average length around 1000bp. I've attached a visual representation...
Forum: Bioinformatics 10-16-2015, 02:23 AM
Replies: 104
Views: 41,706
Posted By gringer
Thanks SNPsaurus. I looked at the examples that...

Thanks SNPsaurus. I looked at the examples that were provided in the first post and assumed that they were the most appropriate way to run the program. It seems a little odd that an assembler would...
Forum: Bioinformatics 10-14-2015, 08:54 PM
Replies: 104
Views: 41,706
Posted By gringer
I expect that this particular method could be...

I expect that this particular method could be replaced by an 'if' statement:


if( ((char >= 'a') && (char <= 'z')) || ((char >= 'A') && (char <= 'Z')) || ((char >= '0') && (char <= '9')) )
Forum: Bioinformatics 10-14-2015, 06:53 PM
Replies: 104
Views: 41,706
Posted By gringer
Ruh roh. Looks like I can't do the merge with...

Ruh roh. Looks like I can't do the merge with Java 1.6:

/media/disk2/bbtools/bbmap/bbmerge.sh in=trimmed_NZGL01795_both_1P.fq.gz in2=trimmed_NZGL01795_both_2P.fq.gz out=merged_assembled.fq...
Forum: Bioinformatics 10-14-2015, 06:23 PM
Replies: 104
Views: 41,706
Posted By gringer
Oh, okay. I guess I missed the "merge" step of...

Oh, okay. I guess I missed the "merge" step of the assembly then. I just looked at the first sentence and didn't realise Tadpole was only an error corrector / extender:
Forum: Bioinformatics 10-13-2015, 04:38 AM
Replies: 104
Views: 41,706
Posted By gringer
For a first-pass effort, I tried just assembling...

For a first-pass effort, I tried just assembling after only trimming (i.e. no host sequence filtering), working off MiSeq 250bp paired-end data:

tadpole.sh in=trimmed_NZGL01795_both_1P.fq.gz...
Forum: Bioinformatics 10-13-2015, 03:40 AM
Replies: 104
Views: 41,706
Posted By gringer
Hmm... option "rinse" for removing bubbles. Very...

Hmm... option "rinse" for removing bubbles. Very clever!
Forum: Bioinformatics 10-12-2015, 04:31 PM
Replies: 104
Views: 41,706
Posted By gringer
Thanks, that's good to know. I'm trying to...

Thanks, that's good to know. I'm trying to assemble a 15-18kb virus (and possibly mitochondria in the future), so that should be fine ;)
Forum: Bioinformatics 10-12-2015, 03:33 PM
Replies: 104
Views: 41,706
Posted By gringer
Will Tadpole (or more generally, your other...

Will Tadpole (or more generally, your other mapping programs) work on a circular genome?
Showing results 1 to 12 of 12

 


All times are GMT -8. The time now is 08:34 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO