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Forum: Sample Prep / Library Generation 08-10-2018, 02:03 PM
Replies: 0
Views: 710
Posted By szy0931
How prepare cell DNA free viral DNA?

I am planning to do WGS to a DNA virus.
How should I prepare virus DNA from the virus stock to avoid contamination from cell DNA?
I think centrifugation or filtration can remove cells but I am...
Forum: Bioinformatics 06-14-2018, 05:24 AM
Replies: 3
Views: 445
Posted By szy0931
Thak you very much! I have one set paired (2...

Thak you very much!
I have one set paired (2 x250) Illumnia MiSeq data from Salmonella.
They look good by FastaQC
I did Unicycler assembling but I did not get a whole genome.
The longest contig...
Forum: Bioinformatics 06-13-2018, 02:04 PM
Replies: 3
Views: 445
Posted By szy0931
Unicycler

I know Unicycler is specialised for bacterial genome assembling from hybrid of short and long reads.
But, is Unicycler also good for bacterial genome assembling only from short reads such as from...
Forum: Bioinformatics 12-13-2016, 10:21 AM
Replies: 0
Views: 709
Posted By szy0931
RNA-Seq for microbiota

I am thinking to study the global gene expression of a particular bacterial species in a microorganism community to see if the presence of other species can affect gene expression of the bacterium.
...
Forum: Bioinformatics 07-11-2016, 12:29 PM
Replies: 1
Views: 953
Posted By szy0931
what is the column of "test_stat" in Cuffdiff output?

what is the column of "test_stat" in Cuffdiff output?
Thank you!
Forum: Bioinformatics 06-20-2016, 11:29 AM
Replies: 1
Views: 567
Posted By szy0931
expression of adjacent genes are affected ?

I am doing RNA-Seq to a mutant strain of Salmonella.
One gene is deleted.
By RNA-Seq, expression of two genes next to the deleted gene is reduced compared with wild type.
The two genes are in one...
Forum: Illumina/Solexa 06-10-2016, 01:38 PM
Replies: 2
Views: 891
Posted By szy0931
Should I combine RNA-Seq results from two sequencings

I am doing bacteria RNA-Seq with Illumina HiSeq.
I did the experiment twice with the same strains.
Each experiment has 3 biological replicates for each strain.
Now I have results from the two...
Forum: Bioinformatics 06-09-2016, 08:12 PM
Replies: 0
Views: 742
Posted By szy0931
Should I combine RNA-Seq results from two sequencings

I am doing bacteria RNA-Seq with Illumina HiSeq.
I did the experiment twice with the same strains.
Each experiment has 3 biological replicates for each strain.
Now I have results from the two...
Forum: Bioinformatics 05-13-2016, 11:19 AM
Replies: 8
Views: 1,752
Posted By szy0931
Thank you very much! Just back from the...

Thank you very much!
Just back from the experiment.
I am reading the links.
Forum: Bioinformatics 05-13-2016, 08:22 AM
Replies: 8
Views: 1,752
Posted By szy0931
I have the following red rights. 1. Per base...

I have the following red rights.
1. Per base sequence content. The first 15 baes have big imbalance and the last base (the 51st) always has much less A. I think removing the last base should be...
Forum: Bioinformatics 05-13-2016, 06:58 AM
Replies: 8
Views: 1,752
Posted By szy0931
after FASTQC, what should we do?

After FASTQC, just like the post in the link (http://rustbeltscientist.tumblr.com/post/38282631404/fastqc-what-tripped-me-up-with-my-first-rna-seq), I feel I do not have too many things to do since...
Forum: Bioinformatics 05-12-2016, 08:24 PM
Replies: 0
Views: 656
Posted By szy0931
what should I do to the overrepresented reads

I have some overrepresented reads in my RNA-Seq for Salmonella
1. ssrA
2. genomic DNA
3. short reads (<20 bp), they are not adapter sequence and were not found in Salmonella genome by blast
What...
Forum: Illumina/Solexa 05-12-2016, 05:47 PM
Replies: 1
Views: 677
Posted By szy0931
short reads are not adapter sequences, why?

I found some short reads in my results. They are apparently shorter than normal reads ( for example ~15 bp vs. 51 bp). But, I found they are not adapter sequences. Why? As I understand, if the inner...
Forum: Bioinformatics 05-12-2016, 08:56 AM
Replies: 0
Views: 624
Posted By szy0931
Questions for Clip adapter sequences

I am analyse my RNA-Seq on Galaxy.
FASTQC results showed me I have overrepresented reads. Many of them are "NNNNNN" and very short reads (<10 bp).
I am using Clip to remove them. (I know clip is...
Forum: Illumina/Solexa 05-12-2016, 06:25 AM
Replies: 7
Views: 784
Posted By szy0931
So, there are two sequencing events happen on a...

So, there are two sequencing events happen on a cluster. One is to sequence the inner cDNA. The other one is to sequence (read) the index to tell the position of the first sequencing event.
Is this...
Forum: Illumina/Solexa 05-12-2016, 06:07 AM
Replies: 7
Views: 784
Posted By szy0931
So, how does the machine or software know which...

So, how does the machine or software know which index is bound to it?
Forum: Illumina/Solexa 05-12-2016, 06:01 AM
Replies: 7
Views: 784
Posted By szy0931
GenoMax, Thank you!

GenoMax,

Thank you!
Forum: Illumina/Solexa 05-12-2016, 05:54 AM
Replies: 7
Views: 784
Posted By szy0931
How does the machine know a read belongs to a certain index?

I have a very basic question.
How does the machine know a read belongs to a certain index?
let's say we have a sequence like this in a single end RNA-Seq:
5' end adapter-cDNA-index-3' end adapter...
Forum: Bioinformatics 01-27-2016, 01:05 PM
Replies: 5
Views: 653
Posted By szy0931
Genomax, I tried the file I edited, but it...

Genomax,

I tried the file I edited, but it did not either.
Now I am thinking the "gap" you mentioned between the two parts in one ID is the cause.
However, I found the RefSeq gff file also has...
Forum: Bioinformatics 01-27-2016, 09:13 AM
Replies: 5
Views: 653
Posted By szy0931
GenoMax, Thank you very much! I do not know...

GenoMax,
Thank you very much!
I do not know bioinformatic too much and I do not know programming.
I just simply searched several gene names appearing in the RefSeq gff file and found they did not...
Forum: Bioinformatics 01-27-2016, 08:33 AM
Replies: 5
Views: 653
Posted By szy0931
update: I unloaded the gff file which did not...

update:
I unloaded the gff file which did not work in GFF3 online validator (http://genometools.org/cgi-bin/gff3validator.cgi) and ran it. I got the following information...
Forum: Bioinformatics 01-26-2016, 01:00 PM
Replies: 5
Views: 653
Posted By szy0931
annotation file did not work

I am working on Salmonella rnaSeq and using Galaxy to analyse data. Here are two sets of assemblies
http://www.ncbi.nlm.nih.gov/assembly/31048
I found the annotation file from RefSeq assembly...
Forum: Bioinformatics 12-14-2015, 02:42 PM
Replies: 3
Views: 804
Posted By szy0931
update: I found a file of feature_table.txt has...

update:
I found a file of feature_table.txt has gene names. How can I convert the feature_table.txt file in to gtf or gff3 file?
Forum: Bioinformatics 12-14-2015, 02:03 PM
Replies: 3
Views: 804
Posted By szy0931
update I just found the gff file I used does...

update
I just found the gff file I used does not have the column gene name though it has gene name described in the last column with other information.
So, I think that is the reason
Forum: Bioinformatics 12-14-2015, 01:49 PM
Replies: 3
Views: 804
Posted By szy0931
cuffdiff does not gene name

Hi, all
I am analyzing my data in Galaxy using bowtie2--cufflinks--cuffmerge--cuffdiff.
I used the annotation gff file in the steps of cufflinks and cuffmerge.
Now in the result of cuffdiff, I...
Showing results 1 to 25 of 36

 


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