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Search took 0.00 seconds. Search: Posts Made By: horvathdp
Forum: Bioinformatics 08-26-2020, 11:58 AM
Replies: 0
Views: 1,202
Posted By horvathdp
samtools view: failed to add PG line to the header

So I get a error when trying to convert my sam to a bam:

samtools view: failed to add PG line to the header

My header seems OK (see below), but I am new at this. How do I fix my headers so my...
Forum: Bioinformatics 02-13-2019, 02:00 PM
Replies: 1
Views: 869
Posted By horvathdp
Why is BBmap throwing java error

Hi all,

I have some myseq data that I want to clean up using bbmap. When I give the following command, I get this error. What is wrong? I am guessing it is having a problem with the sequence I...
Forum: Pacific Biosciences 09-20-2018, 04:47 AM
Replies: 2
Views: 4,806
Posted By horvathdp
Hi, did you eventually come to a good conclusion...

Hi, did you eventually come to a good conclusion with your study? I have a similar situation, and would love to know what worked for you.
Forum: Bioinformatics 06-13-2018, 05:39 AM
Replies: 335
Views: 155,230
Posted By horvathdp
Thanks! for those options, do I just add -tpe...

Thanks! for those options, do I just add -tpe -tbo to the command?
Forum: Bioinformatics 06-12-2018, 09:55 AM
Replies: 335
Views: 155,230
Posted By horvathdp
I have run into a bit of a problem with the...

I have run into a bit of a problem with the adapter trimming. It keeps leaving the sequence "AGATCGG" at the end when I run example:

./bbduk.sh -Xmx1g in1=read1_R1.fastq in2=read1_R2.fastq...
Forum: Bioinformatics 01-04-2018, 06:30 AM
Replies: 12
Views: 4,463
Posted By horvathdp
I am not an expert, but I would bet that when you...

I am not an expert, but I would bet that when you used a kmer of 17, that it collapsed a bit of the genome because the program was not able to easily distinguish between kmers coming from 2 different...
Forum: Bioinformatics 07-12-2017, 10:15 AM
Replies: 12
Views: 4,463
Posted By horvathdp
Your patience and kindness (not to mention the...

Your patience and kindness (not to mention the detailed response) is quite appreciated. Given all the assistance you have been over the years on this project, I feel I should list you as an author...
Forum: Bioinformatics 07-12-2017, 06:15 AM
Replies: 12
Views: 4,463
Posted By horvathdp
Interesting. The genome size as estimated by...

Interesting. The genome size as estimated by flow cytometry was 2.1 Gb. The organism has been reasonably well studied cytogenetically (it is one of the worst invasive weeds in the great plains). It...
Forum: Bioinformatics 07-10-2017, 12:48 PM
Replies: 12
Views: 4,463
Posted By horvathdp
Thanks!!! Here is a link to the data: ...

Thanks!!!

Here is a link to the data:
https://drive.google.com/file/d/0BypoPXNmSy33R0MtMnl2a2NXemM/view?usp=sharing. I didn't know I could define the ploidy level. Can you share a hypothetical...
Forum: Bioinformatics 07-10-2017, 09:43 AM
Replies: 12
Views: 4,463
Posted By horvathdp
Hi All (and particularly Brian Bushnell), I am...

Hi All (and particularly Brian Bushnell),
I am trying to estimate the genome size of my leafy spurge genome with BBMAP. The ouput says my genome size is a haploid of ~950MB. However, using a...
Forum: Bioinformatics 10-21-2016, 10:29 AM
Replies: 15
Views: 6,271
Posted By horvathdp
I am playing with a unix-based option right now....

I am playing with a unix-based option right now. I made a short test list of names in a file test.txt

@HWI-D00653:49:H2FF5BCXX:2:1101:1631:2117 1:N:0:ATCACG...
Forum: Bioinformatics 10-21-2016, 10:18 AM
Replies: 15
Views: 6,271
Posted By horvathdp
NO! sadly, dedupe.sh uses too much memory for my...

NO! sadly, dedupe.sh uses too much memory for my 250G machine for me to run this on my more than 800 million frag file.

Any other ideas that might just sort and remove the duplicates by sequence...
Forum: Bioinformatics 10-18-2016, 08:36 AM
Replies: 15
Views: 6,271
Posted By horvathdp
Yes! Thanks

Yes! Thanks
Forum: Bioinformatics 10-18-2016, 08:17 AM
Replies: 15
Views: 6,271
Posted By horvathdp
In answer to your question above, I did...

In answer to your question above, I did essentially (in some cases when the two different selection protocols identified the same fragment) concat the same file twice. Thus my desire to remove the...
Forum: Bioinformatics 10-18-2016, 08:02 AM
Replies: 15
Views: 6,271
Posted By horvathdp
Ahhh!!! I might have just o=found the answer to...

Ahhh!!! I might have just o=found the answer to my own question:
./dedupe.sh in=concat1.merged out=depuded_concat.merged rmn=t
the rmn=f requires both sequence and identifier to be identical.
...
Forum: Bioinformatics 10-18-2016, 07:32 AM
Replies: 15
Views: 6,271
Posted By horvathdp
Possibly? If that works, then why do people not...

Possibly? If that works, then why do people not just use these essentially 1X files for assembly? I normally see a 20 or 30X coverage for assemblies. This all said, do you know of way to just...
Forum: Bioinformatics 10-18-2016, 06:23 AM
Replies: 15
Views: 6,271
Posted By horvathdp
If I ran dedupe, wouldn't that result in...

If I ran dedupe, wouldn't that result in eliminating all duplicated kmers not just duplicated fragments? I want to assemble the resulting file, and I worry that normalizing the kmer counts to no...
Forum: Bioinformatics 10-18-2016, 05:50 AM
Replies: 15
Views: 6,271
Posted By horvathdp
They were not. They were two different selections...

They were not. They were two different selections (one was a selection of fragments from low copy regions of the genome based on kmers counts and the other a selection of genomic fragments that...
Forum: Bioinformatics 10-17-2016, 03:22 PM
Replies: 15
Views: 6,271
Posted By horvathdp
Removing duplicate fastq entries from concatenated files

I have concatenated two fastq files and I m pretty certain I have quite a few duplicates. Is there a script, program (something in BBMAP?) or common way to remove duplicates based on the sequence...
Forum: Bioinformatics 02-25-2016, 06:18 AM
Replies: 678
Views: 212,291
Posted By horvathdp
Ahh...OK, thanks for using the small words and...

Ahh...OK, thanks for using the small words and simple pictures for my old brain :-). I think I understand the issue. I'll play with this a bit and see what I can teach myself.
Forum: Bioinformatics 02-24-2016, 08:41 AM
Replies: 678
Views: 212,291
Posted By horvathdp
incomplete removal of singletons by BBNORM

Brian (or others),

I am still a bit disturbed by the inability to remove reads that contain singleton kmers. I understand that BBNORM generates an output file that has all reads that contain kmers...
Forum: Bioinformatics 02-27-2015, 09:46 AM
Replies: 0
Views: 882
Posted By horvathdp
best assembler for 160PE and 100PE reads

Hi all,
I have about 60X combined coverage of my genome, but half of my reads are 100 base paired end reads and the other half is 160 base paired end reads. Any suggestions for which assembler would...
Forum: Bioinformatics 02-10-2015, 08:10 AM
Replies: 25
Views: 5,105
Posted By horvathdp
Not sure if I have what i need or not. Looking...

Not sure if I have what i need or not. Looking at Top output, I have 12g in KiB Mem, 11.9G used, 34M free, 7M buffer, KiB swap 52M total, 28M used 23M free, and 21M cached.
Forum: Bioinformatics 02-10-2015, 07:27 AM
Replies: 25
Views: 5,105
Posted By horvathdp
I just ran top to see if it was still thinking,...

I just ran top to see if it was still thinking, and it flashes between 0% memory to 97% use for java, so I am guessing it is still crunching output. The file size is about 68G, but I only have 12Gb...
Forum: Bioinformatics 02-10-2015, 07:00 AM
Replies: 25
Views: 5,105
Posted By horvathdp
Sadly, I am still having an issue (I think). The...

Sadly, I am still having an issue (I think). The program has been running for three days now (but has not appeared to quit) and has the following error messages:
Exception in thread "Thread-45"...
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