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Search: Posts Made By: Illusive Man
Forum: Bioinformatics 08-05-2019, 09:42 AM
Replies: 240
Views: 83,840
Posted By Illusive Man
Dear BBMap users or Brian, I have a...

Dear BBMap users or Brian,

I have a database of about 800 proteins and all I would like to do is create an abundance table of "hits" to these 800 proteins for each one of my 30 samples. Samples...
Forum: Bioinformatics 02-23-2017, 08:14 PM
Replies: 3
Views: 1,538
Posted By Illusive Man
Fastest way to add Ns to variable length sequences to get uniform length

I have a fasta file with a thousand sequences with a distribution of lengths between 100 and 150bp. I would like to add Ns to all sequences whose length is <150. I know it is possible but thus far I...
Forum: Bioinformatics 03-17-2016, 06:55 PM
Replies: 42
Views: 5,266
Posted By Illusive Man
I think I did exactly what you guys stated in the...

I think I did exactly what you guys stated in the earlier scripts I posted. My reference file was already a multi-fasta file containing the three sequences concatenated. When I performed the...
Forum: Bioinformatics 03-16-2016, 09:45 PM
Replies: 42
Views: 5,266
Posted By Illusive Man
I have tried the second command you listed: ...

I have tried the second command you listed:

bash bbmap.sh ref=all.fasta other parameters
Max memory cannot be determined. Attempting to use 3200 MB.
If this fails, please add the -Xmx flag...
Forum: Bioinformatics 03-16-2016, 07:40 PM
Replies: 42
Views: 5,266
Posted By Illusive Man
What do you mean make an index? Do you mean...

What do you mean make an index?

Do you mean a file containing multiple reference sequences that looks like:

>seq1 TAAATGA

>seq2 CCGTTAAA

If that's what you meant then I'm set as I already...
Forum: Bioinformatics 03-16-2016, 01:54 PM
Replies: 42
Views: 5,266
Posted By Illusive Man
Brian or anyone else - Can you tell me if...

Brian or anyone else -


Can you tell me if I can use more than one reference sequence to map my reads too? There are a total of 3 possible genera for the ammonia oxidizing archaea.
Forum: Bioinformatics 03-13-2016, 10:51 AM
Replies: 42
Views: 5,266
Posted By Illusive Man
Bubbas-Mac-Pro:bbmap bubba$ bash bbmap.sh -Xmx10g...

Bubbas-Mac-Pro:bbmap bubba$ bash bbmap.sh -Xmx10g threads=4 ref=amoaref1.fasta in=all_reads.fastq outm=mapped_ref1.fq outu=unmapped.fq nodisk po int rbm don -da
java...
Forum: Bioinformatics 03-09-2016, 10:26 PM
Replies: 42
Views: 5,266
Posted By Illusive Man
Hi Brian - Your da flag seemed to do the trick....

Hi Brian - Your da flag seemed to do the trick. One thing I noticed is that the majority of my read 1 data didn't seem to map very well to the reference archaea sequence (I picked one of the three...
Forum: Bioinformatics 03-09-2016, 12:22 PM
Replies: 42
Views: 5,266
Posted By Illusive Man
Great! I look forward to hearing from him. I...

Great! I look forward to hearing from him. I don't know if it helps any but I also have Geneious 9 and installed the BBMap plugin...maybe I could run part of the workflow in Geneious 9, then do the...
Forum: Bioinformatics 03-09-2016, 12:03 PM
Replies: 42
Views: 5,266
Posted By Illusive Man
Thanks for your help! I tried that but it gave...

Thanks for your help! I tried that but it gave the same error unfortunately...
Exception in thread "main" java.lang.RuntimeException: BBMap terminated in an error state; the output may be corrupt....
Forum: Bioinformatics 03-09-2016, 11:28 AM
Replies: 42
Views: 5,266
Posted By Illusive Man
BBMap version 35.85 Exception in thread "main"...

BBMap version 35.85
Exception in thread "main" java.lang.RuntimeException: Unknown parameter: -threads=4
at align2.AbstractMapper.parse(AbstractMapper.java:627)
at...
Forum: Bioinformatics 03-09-2016, 10:54 AM
Replies: 42
Views: 5,266
Posted By Illusive Man
BBMAP error?

Toms-Mac-Pro:bbmap tomhanks$ bash bbmap.sh -Xmx10g ref=amoa_archaea.fasta in1=Read1.fastq in2=Read2.fastq outm1=mapped_R1.fq outu1=unmapped_R1.fq outm2=mapped_R2.fq outu2=mapped_R2.fq nodisk po int...
Forum: Bioinformatics 03-09-2016, 09:04 AM
Replies: 42
Views: 5,266
Posted By Illusive Man
Is this still the same workflow or is there a...

Is this still the same workflow or is there a simpler process? I have amplicons that are about 634 bp in length, and have read1/read2 sequences that are about 300bp in length, hence there is about a...
Forum: Illumina/Solexa 09-02-2013, 11:45 AM
Replies: 5
Views: 6,971
Posted By Illusive Man
Well based on just the 16S rRNA gene...

Well based on just the 16S rRNA gene approximately 78%, which is what I expected, but that is just a small part of their genome. Do you have any other suggestions in terms of tools?
Forum: Illumina/Solexa 09-02-2013, 11:13 AM
Replies: 5
Views: 6,971
Posted By Illusive Man
Aligning/Mapping Illumina reads to reference in Geneious problem

I am about to give up on this because Geneious just doesn't seem to give me what I am looking for and all the other softwares seem to have a steep learning curve.

I have 4 samples. Each sample has...
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