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Forum: RNA Sequencing 01-12-2015, 11:36 AM
Replies: 0
Views: 962
Posted By michaellim
GalaxyProject-Error Messages

Dear All,

I'm currently using GalaxyProject website's RNA sequencing tools to do my RNA sequencing analyses. However I seem to keep getting the same error messages. I'm unsure what is the problem....
Forum: Bioinformatics 12-25-2014, 05:35 AM
Replies: 348
Views: 194,876
Posted By michaellim
Hi Genomax, Sorry, but I don't understand...

Hi Genomax,

Sorry, but I don't understand what is "/path/to/", if my files are all in C: drive Windows, will it be

jave -ea -Xmx2g in1=C:\sequencing\ST131_1_R1.fastq...
Forum: Bioinformatics 12-24-2014, 05:46 PM
Replies: 348
Views: 194,876
Posted By michaellim
Hi Brian, Got a bit confused with these...

Hi Brian,

Got a bit confused with these commands, so I did RNA sequencing using Truseq Stranded mRNA Kit, 200-bp paired-end.

I understand that I'm supposed to trim the adapters off

*Read 1:...
Forum: RNA Sequencing 12-22-2014, 06:19 PM
Replies: 48
Views: 11,327
Posted By michaellim
Hi Brian, By the way, so for the mapping to...

Hi Brian,

By the way, so for the mapping to work, does that mean, all the FASTQ files and the reference genome (fasta file) must be in the "current" folder or anywhere in the computer?

Thank you
Forum: RNA Sequencing 12-22-2014, 06:15 PM
Replies: 48
Views: 11,327
Posted By michaellim
Hi Brian, Something happened this time, but...

Hi Brian,

Something happened this time, but still something missing? Oh ok, got it. thank you... Silly me.. hahaha

Thank you
Forum: RNA Sequencing 12-22-2014, 06:03 PM
Replies: 48
Views: 11,327
Posted By michaellim
Hi Brian, Here's the picture for you to have...

Hi Brian,

Here's the picture for you to have a look.

Thank you.
Forum: RNA Sequencing 12-22-2014, 05:53 PM
Replies: 48
Views: 11,327
Posted By michaellim
Yup, there is a space. am I missing something?

Yup, there is a space. am I missing something?
Forum: RNA Sequencing 12-22-2014, 05:30 PM
Replies: 48
Views: 11,327
Posted By michaellim
Hi Brian, Yup in C:, copied the entire...

Hi Brian,

Yup in C:, copied the entire command but it states "could not find or load main class align2.bbmap"

any idea what should I do? Maybe you can devise an executable icon file like those...
Forum: Bioinformatics 12-22-2014, 05:05 PM
Replies: 699
Views: 256,569
Posted By michaellim
Hey Guys, If I have Java 8, does that mean I...

Hey Guys,

If I have Java 8, does that mean I can't use BBMap?

Thank you. Merry Christmas
Forum: RNA Sequencing 12-22-2014, 04:56 PM
Replies: 48
Views: 11,327
Posted By michaellim
Thanks Brian, By the way, I've downloaded...

Thanks Brian,

By the way, I've downloaded the BBMap, unzipped it, but I must be not doing it correctly, I cannot seem to find an executable file to click to open the software. Can you please...
Forum: RNA Sequencing 12-22-2014, 03:33 PM
Replies: 48
Views: 11,327
Posted By michaellim
Hi Piet, Does that mean I just paste all the...

Hi Piet,

Does that mean I just paste all the chromosome & plasmid sequence together without breaks using one heading, example

">combinedsequences...
Forum: RNA Sequencing 12-22-2014, 07:31 AM
Replies: 48
Views: 11,327
Posted By michaellim
Hi Genomax, Thank you for the advise, do you...

Hi Genomax,

Thank you for the advise, do you have any recommended handbook/guides/manual/website which teaches some RNA-seq analyses using command lines/softwares?

I would really like to get a...
Forum: RNA Sequencing 12-22-2014, 07:13 AM
Replies: 48
Views: 11,327
Posted By michaellim
Many thanks Piet, appreciate the info for the GFF...

Many thanks Piet, appreciate the info for the GFF file.

Thanks for letting me know, I was unaware of the difference in sequence type. I will give it a go with just the chromosome first. But how do...
Forum: RNA Sequencing 12-20-2014, 05:26 PM
Replies: 48
Views: 11,327
Posted By michaellim
Hi Genomax, Thanks for the explanation. I've...

Hi Genomax,

Thanks for the explanation. I've attached four plots for you to comment. Honestly, I have not much idea about it. All I was told was that as long as the read is above 20 on the Y-axis...
Forum: RNA Sequencing 12-20-2014, 11:29 AM
Replies: 48
Views: 11,327
Posted By michaellim
Hi Brian, Can I get some further...

Hi Brian,

Can I get some further clarification from you too? I was looking at some genomes in NCBI and they are deposited as Chromosome and multiple plasmids.

In this case, when I'm mapping, am...
Forum: RNA Sequencing 12-20-2014, 11:15 AM
Replies: 48
Views: 11,327
Posted By michaellim
Hi Sergio, Yes, I'm truly very grateful for...

Hi Sergio,

Yes, I'm truly very grateful for all the response given. I'm slowly understanding more about the software options and uses and the initial mapping analyses. I have currently no idea as...
Forum: RNA Sequencing 12-20-2014, 11:11 AM
Replies: 48
Views: 11,327
Posted By michaellim
Hi Genomax, Sorry, it's my first time doing...

Hi Genomax,

Sorry, it's my first time doing RNA seq and dealing with sequencing data. I was using MiSeq for the sequencing (the running of the flow cell was done by the sequencing lab, I prepared...
Forum: RNA Sequencing 12-20-2014, 05:54 AM
Replies: 48
Views: 11,327
Posted By michaellim
Hi Sergio, May I check with you whether I...

Hi Sergio,

May I check with you whether I need to trim the adapter sequence from my RNA seq FASTQ file? My Library was about 260 bp each.

Any suggestion how should I do this? Do I just set a...
Forum: RNA Sequencing 12-20-2014, 05:52 AM
Replies: 48
Views: 11,327
Posted By michaellim
Dear All, May I also ask, since my RNA seq...

Dear All,

May I also ask, since my RNA seq libraries were about 260 bp in size according to Illumina's preparation protocol, for the FASTQ files which I've currently have, do I need to remove the...
Forum: RNA Sequencing 12-20-2014, 05:50 AM
Replies: 48
Views: 11,327
Posted By michaellim
Hi Piet, I see, I have close to none...

Hi Piet,

I see, I have close to none coding/programming knowledge, then maybe BWA is not suitable then. But I will check out the website for more info about it.

I did consider DNA sequencing...
Forum: RNA Sequencing 12-19-2014, 01:37 PM
Replies: 48
Views: 11,327
Posted By michaellim
Hi Piet, Many thanks for the clarification....

Hi Piet,

Many thanks for the clarification. I will give it a try with different genomes then if it doesn't take too long. May I know what kind of alignment/mapping software do you use? Is there...
Forum: RNA Sequencing 12-19-2014, 08:44 AM
Replies: 48
Views: 11,327
Posted By michaellim
Thanks Brian for the info. I will give it a...

Thanks Brian for the info.

I will give it a go first and see what happens.
Forum: RNA Sequencing 12-19-2014, 08:44 AM
Replies: 48
Views: 11,327
Posted By michaellim
Hi Sergioo, Yes, MLST. For example, E.coli...

Hi Sergioo,

Yes, MLST. For example, E.coli ST11 will be different from ST131. However, we aren't certain whether there is any genes which is specific to ST131 which cannot be found in other E....
Forum: RNA Sequencing 12-18-2014, 05:50 PM
Replies: 48
Views: 11,327
Posted By michaellim
Hi GenoMax, Thanks for the info. Could you...

Hi GenoMax,

Thanks for the info. Could you please advise how do I compare the "Published completed genome" with the other "published genome which is in contigs", do I need to merge the contigs...
Forum: RNA Sequencing 12-18-2014, 05:46 PM
Replies: 48
Views: 11,327
Posted By michaellim
Hi Brian, So if I were to use the multiple...

Hi Brian,

So if I were to use the multiple contigs for my reference when aligning my RNAseq data, may I ask how should I do this? Do I need to first combine all the contigs (how can I do this?)?
...
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