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Forum: RNA Sequencing 09-28-2017, 06:00 PM
Replies: 0
Views: 1,407
Posted By neokao
rnacocktail basic questions

My lab typically does RNA-seq ~once a year and I do the bioinformatic analysis myself. So the annoying part for me being not the expert in routine NGS analysis from raw data, every time I get new...
Forum: Metagenomics 07-02-2016, 09:07 PM
Replies: 4
Views: 1,842
Posted By neokao
Thanks for the reply, Brian. As I mentioned, we...

Thanks for the reply, Brian. As I mentioned, we have done 16S and WGS on our mouse gut/fecal microbiota already. I actually don't care about the differences before and after culturing. What we need...
Forum: Metagenomics 07-01-2016, 03:49 PM
Replies: 4
Views: 1,842
Posted By neokao
Culturable microbiome NGS

My lab has done 16S and whole genome shotgun on mouse gut/fecal microbiome (wild-type vs knockout). Recently we found that the culturable part of these knockout mouse fecal samples are actually...
Forum: Metagenomics 08-29-2015, 07:11 PM
Replies: 0
Views: 1,523
Posted By neokao
Redundancy analysis (RDA) heatmap for 16s NGS results

My lab has been working on bacterial 16S-based microbiome analysis in mouse gut and fecal samples. We are trying make figures like the attached pdf file.
I have seen several figures (based on...
Forum: Metagenomics 06-16-2015, 06:56 AM
Replies: 4
Views: 6,481
Posted By neokao
Thanks for the suggestions. I agree and my goal...

Thanks for the suggestions. I agree and my goal is quite simple:
I have a knock-out mouse with a special gut microbiota-associated phenotype. So I'd like to know the difference (bacterial species...
Forum: Metagenomics 06-08-2015, 07:28 PM
Replies: 4
Views: 6,481
Posted By neokao
shotgun metagenomic sequencing coverage

My lab has been working on bacterial 16S-based microbiome analysis in mouse gut and fecal samples. Recently I've been thinking to move on to Illumina shotgun metagenomic sequencing if we could...
Forum: Bioinformatics 04-09-2015, 03:31 AM
Replies: 218
Views: 142,350
Posted By neokao
I did : /usr/local/Cellar/gcc49/bin/g++-4.9 -v...

I did : /usr/local/Cellar/gcc49/bin/g++-4.9 -v and got this:
-bash: /usr/local/Cellar/gcc49/bin/g++-4.9: No such file or directory.

Anyway, I downloaded your 2.4.0k Mac executable and it worked...
Forum: Bioinformatics 04-07-2015, 08:38 PM
Replies: 218
Views: 142,350
Posted By neokao
i switched to source directory. grep...

i switched to source directory.
grep STARforMacStatic Makefile
STARforMacStatic : CCFLAGS=-D'COMPILE_FOR_MAC' -I ./Mac_Include/ $(CCFLAGS_main)
STARforMacStatic : parametersDefault.xxd $(OBJECTS)...
Forum: RNA Sequencing 04-07-2015, 07:43 PM
Replies: 5
Views: 1,908
Posted By neokao
It turned out the issue is on the "factor". ...

It turned out the issue is on the "factor".

I followed the Bioconductor's suggestion and did:

> deg_01$newMGI_symbol <- convertIDs(as.character(deg_01$id), "REFSEQ", "SYMBOL", org.Mm.eg.db)
...
Forum: Bioinformatics 04-07-2015, 04:43 AM
Replies: 218
Views: 142,350
Posted By neokao
I used homebrew to install gcc again. The...

I used homebrew to install gcc again. The installed path is /usr/local/Cellar/gcc49.

Then I did make STARforMacStatic CXX=/usr/local/Cellar/gcc49/bin/g++-4.9 and I got another error:
make: ***...
Forum: RNA Sequencing 04-06-2015, 05:14 PM
Replies: 5
Views: 1,908
Posted By neokao
> class(deg_01$id) [1] "factor" >...

> class(deg_01$id)
[1] "factor"
> head(deg_01$id)
[1] NM_026268 NM_025777 NM_013478 NR_015524 NM_001099297 NM_177610
142 Levels: NM_001004140 NM_001005423 NM_001014976 NM_001024139...
Forum: RNA Sequencing 04-06-2015, 02:59 PM
Replies: 5
Views: 1,908
Posted By neokao
I actually did this first: >...

I actually did this first:

> deg_01$newMGI_symbol <- convertIDs(deg_01$id, "REFSEQ", "SYMBOL", org.Mm.eg.db)

Error in .testForValidKeys(x, keys, keytype) :
'keys' must be a character...
Forum: RNA Sequencing 04-05-2015, 04:35 PM
Replies: 5
Views: 1,908
Posted By neokao
gene level analysis (lincRNA, pseudogenes) ?

Hey, there,

I used STAR and featurecounts on 20 mouse samples from RNAseq.
With many helps from the forums, now I got lists of DEGs.

I realized that there are quite some lincRNA pseudogenes in...
Forum: RNA Sequencing 04-05-2015, 04:22 PM
Replies: 6
Views: 2,236
Posted By neokao
Thanks dpryan. I finally did it with STAR and...

Thanks dpryan. I finally did it with STAR and featurecounts.
I have some following questions posted with a different topic.
Forum: Bioinformatics 04-02-2015, 04:58 PM
Replies: 218
Views: 142,350
Posted By neokao
Yes. My gcc is there. So I did make...

Yes. My gcc is there.
So I did make STARforMacStatic CXX=/usr/bin/gcc but still got error:

clang: error: unsupported option '-static-libgcc'
make: *** [STARforMacStatic] Error 1

Thanks folks.
Forum: Bioinformatics 04-02-2015, 02:24 PM
Replies: 218
Views: 142,350
Posted By neokao
Following your suggestion, I got a different...

Following your suggestion, I got a different error:
/bin/sh: /path/to/gcc: No such file or directory
make: *** [Depend.list] Error 127

I did install gcc.
gcc --version
Configured with:...
Forum: Bioinformatics 04-02-2015, 07:04 AM
Replies: 218
Views: 142,350
Posted By neokao
I did have SAMTOOLS installed. Say under my NGS...

I did have SAMTOOLS installed. Say under my NGS folder, I have samtools-1.2 folder and STAR-STAR_2.4.0k folder. I did STARforMac in the source directory (in STAR-STAR_2.4.0k).
Any advice? Thanks.
Forum: Bioinformatics 04-02-2015, 06:03 AM
Replies: 218
Views: 142,350
Posted By neokao
I tried that particular .fq file using old STAR...

I tried that particular .fq file using old STAR with SAM output and then it went through.
I still want to test your new version.
(Thanks for your new code.) However, I got error when I tried to...
Forum: Bioinformatics 03-31-2015, 07:02 AM
Replies: 218
Views: 142,350
Posted By neokao
I guess so too. I manually did these 20 .fq files...

I guess so too. I manually did these 20 .fq files with occasional Killed: 9 error. I found that it could usually go through if I run the EXACT code again (even without rebooting the OSX). However now...
Forum: Bioinformatics 03-29-2015, 07:51 PM
Replies: 218
Views: 142,350
Posted By neokao
Thanks, Alex. I don't know what's causing...

Thanks, Alex.

I don't know what's causing the problem for multi-threading on my Mac mini.
I got the same error even after I rebooted the computer and started the mapping freshly.

Anyways, I...
Forum: Bioinformatics 03-28-2015, 02:38 PM
Replies: 218
Views: 142,350
Posted By neokao
So it went through successfully. With the code...

So it went through successfully. With the code like this:
> STAR --genomeDir ./GenomeDir/ --readFilesIn...
Forum: Bioinformatics 03-27-2015, 05:17 PM
Replies: 218
Views: 142,350
Posted By neokao
Somehow I could not send private message...

Somehow I could not send private message successfully, the new log.out file is in this link https://app.box.com/s/0nqn3jknqq1ta66jl1evme8c8ldunq9k

I guess that the issue started when it was...
Forum: Bioinformatics 03-26-2015, 09:36 PM
Replies: 218
Views: 142,350
Posted By neokao
Hey, Alex: Just tried with reindexing...

Hey, Alex:

Just tried with reindexing genome.
Code:
STAR --runMode genomeGenerate --genomeDir ./GenomeDir --genomeFastaFiles ./Mus_musculus.GRCm38.dna.primary_assembly.fa --runThreadN 8...
Forum: Bioinformatics 03-26-2015, 05:47 PM
Replies: 218
Views: 142,350
Posted By neokao
Hey, I just switched from BWA to STAR for my...

Hey,

I just switched from BWA to STAR for my RNAseq analysis yesterday. I got stuck with this: Mar 27 08:14:36 ..... Started STAR run
Mar 27 08:24:33 ..... Started mapping
Killed: 9

Then STAR...
Forum: RNA Sequencing 03-26-2015, 01:29 AM
Replies: 6
Views: 2,236
Posted By neokao
I thought STAR is adapted to align long reads....

I thought STAR is adapted to align long reads. Mine are short reads. I guess I might be wrong.
Regarding the Ensembl reference genome/transcriptome for mouse RNAseq, is the...
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