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Forum: Bioinformatics 04-12-2020, 04:57 PM
Replies: 53
Views: 38,409
Posted By silverfox
normalized reads file empty

Hi Brian and everyone! I'm using bbnorm but i keep getting a problem.

I ran the command:

$ bbnorm.sh -Xmx64g t=18 in=pt.raw.fastq out=pt.raw.normalized.fq target=90 mindepth=2

everything...
Forum: Bioinformatics 04-10-2020, 02:42 PM
Replies: 53
Views: 38,409
Posted By silverfox
Hi!!! A question, please. BBNorm can also be...

Hi!!! A question, please.

BBNorm can also be used to normalize the coverage of PacBio reads??

Thank you in advance!

edited:
I just read that it indeed can be used on PacBio reads but...
Forum: Bioinformatics 07-27-2019, 02:57 PM
Replies: 104
Views: 36,526
Posted By silverfox
Hi GenoMax! Thank you for your reply! My...

Hi GenoMax! Thank you for your reply!

My libraries were not made from isolated mitochondria and chloroplast DNA. We made a whole genome sequencing of purple maize. Then I mapped all the reads...
Forum: Bioinformatics 07-27-2019, 08:47 AM
Replies: 104
Views: 36,526
Posted By silverfox
Hi! I'm assembling a chloroplast and a...

Hi! I'm assembling a chloroplast and a mitocondrial genome :)

I was using the reads that mapped agains a close reference for both, and doing de novo assembly. I plan to extend my read length and...
Forum: Bioinformatics 07-27-2019, 07:45 AM
Replies: 104
Views: 36,526
Posted By silverfox
I have a lot more reads. The ones used in the...

I have a lot more reads. The ones used in the assembly with SPAdes were a just a sampling (to have a 60x coverage of my reference genome, of 569630 bp).
These reads data that I gave tadpole are...
Forum: Bioinformatics 07-26-2019, 08:35 PM
Replies: 104
Views: 36,526
Posted By silverfox
Hi! I have two sets of reads: mit_1.fastq y...

Hi! I have two sets of reads: mit_1.fastq y mit_2.fastq (I'm assembling a mitogenome) and I want to use them to extend my contigs.

Extending contigs with reads could be done like this:
...
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