SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 500
Search took 0.06 seconds.
Search: Posts Made By: GenoMax
Forum: Bioinformatics Yesterday, 07:21 AM
Replies: 219
Views: 66,534
Posted By GenoMax
Let us know if using more memory made a...

Let us know if using more memory made a difference.

You should really be using a different tool designed for long read alignments. Even LASTZ may be appropriate since you have query sequences as...
Forum: Bioinformatics 02-21-2019, 03:45 PM
Replies: 219
Views: 66,534
Posted By GenoMax
@grammtonotus: How much memory are you allocating...

@grammtonotus: How much memory are you allocating for this job? With that large sized fragments you are likely going to need plenty.

I also suggest that you look into using `minimap2` from Heng Li...
Forum: General 02-19-2019, 05:41 PM
Replies: 5
Views: 293
Posted By GenoMax
You could perhaps ask for a former labmate to...

You could perhaps ask for a former labmate to send you one? As they say a picture is worth a thousand words.
Forum: RNA Sequencing 02-19-2019, 12:48 PM
Replies: 2
Views: 121
Posted By GenoMax
Samtools 1.9 is the latest version.

Samtools 1.9 is the latest version.
Forum: Epigenetics 02-19-2019, 10:35 AM
Replies: 1
Views: 113
Posted By GenoMax
Have you looked at deepTools...

Have you looked at deepTools (https://deeptools.readthedocs.io/en/develop/ )?
Forum: RNA Sequencing 02-19-2019, 10:34 AM
Replies: 5
Views: 115
Posted By GenoMax
Looks good!

Looks good!
Forum: RNA Sequencing 02-19-2019, 10:15 AM
Replies: 5
Views: 115
Posted By GenoMax
Oops. I should have looked at the error...

Oops. I should have looked at the error carefully. You are correct.

Edit: Found the problem. You have a space between clipped and file name here (clipped/ SRR359063_2.fastq.zip ). Remove that.
Forum: RNA Sequencing 02-19-2019, 09:57 AM
Replies: 5
Views: 115
Posted By GenoMax
STAR requires a lot of RAM depending on genome...

STAR requires a lot of RAM depending on genome size. e.g. human genome will need ~30G of free RAM which you may not have available on your Mac. If that is true, you will not be able to do this on...
Forum: General 02-19-2019, 06:31 AM
Replies: 5
Views: 293
Posted By GenoMax
Post a picture perhaps?

Post a picture perhaps?
Forum: RNA Sequencing 02-18-2019, 04:57 PM
Replies: 2
Views: 125
Posted By GenoMax
This is the critical piece. TopHat is not finding...

This is the critical piece. TopHat is not finding some file/directory that you specified in your command. Since you have not included your full command you will need to investigate which it may be.
Forum: Bioinformatics 02-18-2019, 04:39 AM
Replies: 93
Views: 18,242
Posted By GenoMax
@DCZ: That is easy to do. If you do not provide...

@DCZ: That is easy to do. If you do not provide any "out=" argument to most BBTools they will do the operation and produce relevant statistics without writing the output.

Tip: If you ever want to...
Forum: RNA Sequencing 02-14-2019, 02:13 PM
Replies: 2
Views: 250
Posted By GenoMax
Open any web browser you like and then navigate...

Open any web browser you like and then navigate to that html file and open it. There is nothing special about firefox.
Forum: Bioinformatics 02-14-2019, 06:50 AM
Replies: 31
Views: 18,479
Posted By GenoMax
You could use `repair.sh` to separate the...

You could use `repair.sh` to separate the singletons out afterwards.
Forum: Bioinformatics 02-13-2019, 04:34 PM
Replies: 1
Views: 170
Posted By GenoMax
Can you try running by specifying the memory by...

Can you try running by specifying the memory by adding "-Xmx4g" to your command?
Forum: RNA Sequencing 02-13-2019, 04:29 PM
Replies: 4
Views: 203
Posted By GenoMax
Correct. That executable is likely in the "bin"...

Correct. That executable is likely in the "bin" directory that you see above. So you could have run it by saying $ bin/fastq-dump --outdir raw/ --split-3 --gzip SRR359063
Forum: RNA Sequencing 02-13-2019, 12:45 PM
Replies: 4
Views: 203
Posted By GenoMax
The directory you have the program "fastq-dump"...

The directory you have the program "fastq-dump" is likely not in your $PATH ( a set of directories that are automatically searched when you try to run something). You could try ./fastq-dump if the...
Forum: Bioinformatics 02-12-2019, 12:40 PM
Replies: 8
Views: 274
Posted By GenoMax
I am wondering if the error you are seeing is a...

I am wondering if the error you are seeing is a red herring. How much memory are you allocating to this job on the cluster (bbsplit can need a lot of memory depending on size of the reference...
Forum: Bioinformatics 02-12-2019, 10:09 AM
Replies: 8
Views: 274
Posted By GenoMax
Can you validate your fastq files to make sure...

Can you validate your fastq files to make sure there are no errors in the file?

Use validateFiles (http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/validateFiles)from Kent Utilities (UCSC)....
Forum: Bioinformatics 02-11-2019, 03:20 PM
Replies: 8
Views: 274
Posted By GenoMax
BBSplit will take fastq reads and bin them. Let...

BBSplit will take fastq reads and bin them. Let me know how that works.

You can convert the merged fastq reads afterwards with reformat.sh in=merged.fq.gz out=merged.fa No paste/cut/sed needed...
Forum: Bioinformatics 02-11-2019, 12:26 PM
Replies: 8
Views: 274
Posted By GenoMax
Do you get an error right away or does the...

Do you get an error right away or does the program run for some time?

Are these bbmerged reads? Wonder if you should try to do the binning with original fastq data. Is that a possibility?
Forum: Bioinformatics 02-11-2019, 12:23 PM
Replies: 1
Views: 239
Posted By GenoMax
Are you sure about tablet not being able to open...

Are you sure about tablet not being able to open more than one alignment?

In any case IGV will allow you to open multiple files (aligned to same genome). You will need to make sure you have enough...
Forum: Bioinformatics 02-10-2019, 04:59 PM
Replies: 1
Views: 205
Posted By GenoMax
You could use "reformat" from BBMap suite. It...

You could use "reformat" from BBMap suite. It will work in Windows as long as you have Java 1.8. Look at the sampling parameters to select an appropriate one.
Forum: Bioinformatics 02-07-2019, 04:46 AM
Replies: 320
Views: 96,023
Posted By GenoMax
We are making progress! How much memory do...

We are making progress!

How much memory do you have on this Mac? I suggest using 85% of the maximum memory you have available with BBTools. You also need to specify "in1= and out1=" to go with...
Forum: Bioinformatics 02-06-2019, 09:31 AM
Replies: 320
Views: 96,023
Posted By GenoMax
On a Mac I tested this on nothing else was needed...

On a Mac I tested this on nothing else was needed to be done. What happens if you just run "bbmap.sh". Does that produce "in-line" bbmap help output?

Which Java version are you using on your Mac?
Forum: Bioinformatics 02-06-2019, 05:52 AM
Replies: 320
Views: 96,023
Posted By GenoMax
I am not sure why you are having this problem....

I am not sure why you are having this problem. All you should need to do is download BBMap software on your mac. Unarchive the tar-zipped file and then extend your path to include the "bbmap"...
Showing results 1 to 25 of 500

 


All times are GMT -8. The time now is 12:39 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO