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Search: Posts Made By: DrYak
Forum: Bioinformatics 03-20-2018, 02:17 AM
Replies: 37
Views: 32,023
Posted By DrYak
Hi, Can I use reformat or any other bbtools...

Hi,

Can I use reformat or any other bbtools script to split my fasta file into sub-files?

eg X.fa (100 sequences) -> X01.fa X02.fa....X10.fa (each with 10 sequences)?

I don't mind whether I...
Forum: Bioinformatics 03-02-2018, 05:47 AM
Replies: 5
Views: 2,936
Posted By DrYak
Smile worked finally - but had to increase kmer and literal..

Hi,

Thank you, I finally got it to work with literal, but I had to increase the length of the literal to 20 X T and increase the kmer to 25. With literal=TTTTTTTT k=5 I got 98% of the reads...
Forum: Bioinformatics 02-18-2018, 11:08 PM
Replies: 5
Views: 2,936
Posted By DrYak
Hi, Thank you for the suggestion. With...

Hi,

Thank you for the suggestion.

With the "-Xmx24052m threads=12" flag it runs with 12 threads and the memory but still has an ArrayIndexOutOfBoundsException in multiple threads...
:confused:...
Forum: Bioinformatics 02-15-2018, 06:37 AM
Replies: 5
Views: 2,936
Posted By DrYak
Question BBDuk java error when filtering using entropy?

Hello,

I am having an issue with a java error when trying to use BBDuk to remove low entropy sequences from a fastq file. The libraries were made using ribozero so there are a number of polyT...
Forum: Bioinformatics 02-14-2018, 02:28 AM
Replies: 335
Views: 155,155
Posted By DrYak
Question Entropy filtering: Java ArrayIndexOutOfBoundsException

Hi,

I'm having an issue while trying to filter a fastq file using an entropy filter. The library protocol used ribozero so there are a lot of poly T sequences that I would like to remove.

I...
Forum: Bioinformatics 07-04-2016, 10:54 PM
Replies: 2
Views: 2,184
Posted By DrYak
Wink I must admit I was hoping and, quite frankly,...

I must admit I was hoping and, quite frankly, expecting, that BBMap would be capable of this. Once again thank you for your excellent package...

Yours,
Dave
Forum: Bioinformatics 07-04-2016, 07:12 AM
Replies: 2
Views: 2,184
Posted By DrYak
Question GC content of assembled transcripts

Hi,

I have a transcriptome assembly that is comprised of a metazoan and protist (intracellular symbiont) component. I know from the assemblies of similar organisms that the CG percentage of the...
Forum: Bioinformatics 04-07-2016, 07:58 AM
Replies: 2
Views: 2,105
Posted By DrYak
Hi, Well, I found (to my chagrin) that...

Hi,

Well, I found (to my chagrin) that cd-hit has an aux tools package containing the cd-hit-dup tool.

I do not, however, get the same results using cd-hit-est and cd-hit-dup.

If I use...
Forum: Bioinformatics 04-07-2016, 06:58 AM
Replies: 2
Views: 2,105
Posted By DrYak
Dedupe on assembled RNA-Seq?

Hi,

I am trying to get rid of "redundant" sequences from a trinity assembly. I used dedupe.sh to get rid of duplicates in the illumina source files and got a very good result.

After assembling...
Forum: Bioinformatics 10-02-2015, 05:39 AM
Replies: 3
Views: 1,793
Posted By DrYak
Talking faSomeRecords = lifesaver

Thank you so much genomax - that took less than 2 seconds for each file. The other way was still chugging away after two days...
Forum: Bioinformatics 10-02-2015, 04:33 AM
Replies: 3
Views: 1,793
Posted By DrYak
Question Subsetting a fasta file based on a set of BLAST results

Hi,

I have assembled a de novo transcriptome from my species of interest using trinity. The species has an internal symbiont (algae) and those sequences were obviously sequenced along with it. I...
Forum: Illumina/Solexa 09-06-2013, 02:44 AM
Replies: 2
Views: 4,340
Posted By DrYak
Question RNA-seq on MiSeq - enough depth of cover for a novel 500 MB genome?

Hi,

I'm looking to do DGE on an eukaryotic genome of around 450-500MB. It is on an unsequenced species although there are related species that have draft and transcriptome data available. I was...
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