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Forum: Bioinformatics 11-06-2015, 09:12 AM
Replies: 12
Views: 2,404
Posted By syintel87
Genome size estimation using BBMAP

Hi all,
I have 21,005,534 x 2 paired-end genome sequencing data.
To estimate the genome size, I used BBMAP.
Is there anyone who could help to interpret the output?

The command: ...
Forum: Bioinformatics 03-06-2015, 09:33 AM
Replies: 5
Views: 1,070
Posted By syintel87
Ah, now I see! In formats "0, 1, and 3", dots...

Ah, now I see! In formats "0, 1, and 3", dots stand for identities between query and target. And differences are shown with protein letters.

I should have posted after more consideration.
Thanks...
Forum: Bioinformatics 03-06-2015, 09:21 AM
Replies: 5
Views: 1,070
Posted By syintel87
In addition to "-outfmt 1", I tried other options...

In addition to "-outfmt 1", I tried other options as well.
There seem to be different ways of alignment.

0 = pairwise
1 = query-anchored showing identities
2 = query-anchored no identities
3 =...
Forum: Bioinformatics 03-06-2015, 08:26 AM
Replies: 5
Views: 1,070
Posted By syintel87
My query sequences are contigs that are de novo...

My query sequences are contigs that are de novo assembled, some of which are short (e.g. 500) whereas others are very long (e.g. 100,000).

But database of blast is composed of several peptide...
Forum: Bioinformatics 03-05-2015, 12:35 PM
Replies: 5
Views: 1,070
Posted By syintel87
tblastx fmt1 Output Interpretation

Hello,
While locally running "blastx" with output option "-outfmt 1", I have a question.

The below is an example of my result. As seen, throughout the outputs, all pairs of anchored proteins are...
Forum: Bioinformatics 05-23-2014, 08:32 AM
Replies: 1
Views: 728
Posted By syintel87
Gene Ontology Program

Hi,
I have de novo assembled contigs in fasta file.
And I have been running blast2go for several weeks.
However, it is too slow. Only 4% of blast search has been done until now.

Would you...
Forum: Bioinformatics 05-01-2014, 08:48 AM
Replies: 0
Views: 723
Posted By syintel87
[SOAPdenovo] coverage cut off

Hello.
While running SOAPdenovo assembler, I have a question about parameter setting.

What I want to do are set different coverage cut offs and compare the results.
So the commands that I used...
Forum: Bioinformatics 02-16-2014, 03:42 AM
Replies: 1
Views: 2,558
Posted By syintel87
[Gene Prediction] AUGUSTUS program

Hello, I am running AUGUSTUS which is a program for gene prediction.
If there is someone who has experience of using this program, would you help me?

- My organism: Meloidogyne Chitwoodi
- What...
Forum: Bioinformatics 02-13-2014, 06:35 PM
Replies: 1
Views: 782
Posted By syintel87
[GlimmerHMM] anyone who has successfully run?

Hello,
I have been trying to run "trainGlimmerHMM" for several weeks.
However, error message keeps occurring.

Though I ran a real example of fasta and cds files which is given in the instruction...
Forum: Bioinformatics 02-06-2014, 02:00 PM
Replies: 1
Views: 1,199
Posted By syintel87
ERROR MESSAGE: CODE: line 338 is...

ERROR MESSAGE:



CODE: line 338 is underlined and in red.
Forum: Bioinformatics 02-06-2014, 01:30 PM
Replies: 1
Views: 1,199
Posted By syintel87
[GlimmerHMMJ] error message

Hello,
When I ran "trainGlimmerHMM", my job was exited.
Would you please give me a piece of advice if you have any idea about the error message?
The error message says:

Training data created...
Forum: Bioinformatics 02-05-2014, 11:10 AM
Replies: 1
Views: 1,132
Posted By syintel87
I want to clarify my question above. If I...

I want to clarify my question above.
If I choose to run trainGlimmerHMM, would you see if my understanding is right?
Would you see the description below again to see if my understanding is right?...
Forum: Bioinformatics 02-05-2014, 05:34 AM
Replies: 1
Views: 1,132
Posted By syintel87
[GlimmerHMM] Is my understanding right?

Hello, I have a question on GlimmerHMM.
Would you have a look at the description below to see if my understanding is right?
My organism is M. Chitwoodi.
Thank you in advance.

1. What I have as...
Forum: Bioinformatics 02-01-2014, 12:14 PM
Replies: 1
Views: 761
Posted By syintel87
de novo assembly & gene prediction

Hello,

- I did de novo assembly of M. Chitwoodi, by using "Abyss" program.
- Then I've got the longest contig in fasta file.
- When I did blast with the longest contig, I could see some results....
Forum: Bioinformatics 01-13-2014, 05:37 AM
Replies: 0
Views: 1,278
Posted By syintel87
[Abyss de novo assembly] setting 127 k-mer length

"How to set kmer length as 127?"

Hello, I have a problem with setting kmer length as 127.

1. The codes below gave errors.


2. So I made a change with the codes.
Forum: Bioinformatics 01-13-2014, 04:51 AM
Replies: 1
Views: 959
Posted By syintel87
[SOAPdenovo] used and unused reads

Hello, I am using SOAPdenovo program.
I'd like to know how many reads were used and unused in denovo assembly.
When looking into "scafStatistics" file, I have no idea about how to extract those...
Forum: Bioinformatics 10-11-2013, 09:33 PM
Replies: 3
Views: 4,429
Posted By syintel87
[velvetg] segmentation fault?

Hello,

- I am running "velvet".
- Velvet that I am using is the latest version.
- After running velvetg, I've got error message "segmentation fault".
- I think the memory is enough: I can use...
Forum: Bioinformatics 10-04-2013, 09:32 AM
Replies: 8
Views: 3,372
Posted By syintel87
[Velvet] multiple files from each library

I have questions about running "Velvet".
What I want to do is de novo assembly with short read sequence.

Data Description:
- I have fastq files generated from Illumina.
- These are paired end...
Forum: Bioinformatics 07-30-2013, 02:13 PM
Replies: 0
Views: 554
Posted By syintel87
[R - Bioconductor] TSSi error message

Hello,

While running TSSi, error has kept occuring.
The error message says, "Error in .local(counts, start, end, chr, region, strand, replicate, annotation, : Duplicated start positions within...
Forum: Bioinformatics 06-17-2013, 02:18 PM
Replies: 0
Views: 879
Posted By syintel87
[HTSeq-Count] How are reads counted?

I have questions about how htseq-count software counts reads.

What I wonder is...
When are reads not counted but ignored from counting?
When are reads counted as 1?
How many mapped reads are...
Forum: Bioinformatics 05-23-2013, 07:12 PM
Replies: 0
Views: 1,095
Posted By syintel87
[EdgeR] exactTest dispersion="common"

While doing exactTest in EdgeR,
I can choose an option, dispersion= "common", "tagwise", or "auto".
My question is what is the difference between these two options. Which option is appropriate?
...
Forum: Bioinformatics 05-03-2013, 06:42 AM
Replies: 16
Views: 1,771
Posted By syintel87
In the first place, I dealt with 7 time points...

In the first place, I dealt with 7 time points separately and ran edgeR without replicate. Though there was no replicate, among 21 pairwise tests, one pairwise test of "egg and juvenile" provided the...
Forum: Bioinformatics 05-03-2013, 06:36 AM
Replies: 16
Views: 1,771
Posted By syintel87
Anyhow, I still wonder why my plot of...

Anyhow, I still wonder why my plot of (p-value,count) looks like zigzag. In normal case, doesn't this happen? Is this because of my unstable data set?

Also, p-value distribution does not look bad,...
Forum: Bioinformatics 05-03-2013, 06:15 AM
Replies: 16
Views: 1,771
Posted By syintel87
1. Yes, I meant that in T2, the vast majority of...

1. Yes, I meant that in T2, the vast majority of your reads map to the host, and only a percent or so map to the worm genome. I am so sorry for not having mentioned that.

2. Actually, I have seven...
Forum: Bioinformatics 05-03-2013, 06:14 AM
Replies: 16
Views: 1,771
Posted By syintel87
Thank you so much for advice.

Thank you so much for advice.
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