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Search: Posts Made By: yifangt
Forum: Bioinformatics 12-08-2015, 12:52 PM
Replies: 11
Views: 9,049
Posted By yifangt
bcl2fastq installation failed

Hello,
I met the same problem when installing bcl2fastq-v2.17.1.14 from source.
Tried suggestions from this post, none worked.
It seems related to boost library as it tried to install boost_1_54_0...
Forum: Bioinformatics 09-15-2015, 02:12 PM
Replies: 17
Views: 10,816
Posted By yifangt
Thanks a lot! Each time we upgrade the box, or...

Thanks a lot!
Each time we upgrade the box, or switch to new box, I have to come here to recall the details.
Forum: Bioinformatics 06-18-2015, 03:20 PM
Replies: 52
Views: 22,447
Posted By yifangt
IMAGE manual

Hello,
Can anyone share your experience using IMAGE for gap closing. I could not get it run after a couple of hours try. I need you explain the options for IMAGE command line for me, ...
Forum: Bioinformatics 12-12-2014, 08:40 AM
Replies: 13
Views: 3,221
Posted By yifangt
SSPACE merge contigs

Hello, rhinoceros!
Could you please post your script or cammand line to merge contigs with SSPACE? I'm doing similar thing. Thanks in advance!
Forum: 454 Pyrosequencing 10-20-2014, 09:38 PM
Replies: 13
Views: 10,115
Posted By yifangt
Newbler installation v3.0

Thanks Sven!
1) I finally get it installed locally. I did not try that option before and today I gave it a try and it worked! I have the root permission for my box, but I do not understand why it...
Forum: 454 Pyrosequencing 10-16-2014, 09:52 AM
Replies: 13
Views: 10,115
Posted By yifangt
Thanks! Yes, I tried to setup thru command...

Thanks!
Yes, I tried to setup thru command line. And the only error message is the failed dependencies, no other output.
Where did you get the package DataProcessing_3.0.tgz? I went to Roche...
Forum: 454 Pyrosequencing 10-13-2014, 06:49 PM
Replies: 13
Views: 10,115
Posted By yifangt
Thanks skalges! Here it is:yifangt@spade:~$ ls -l...

Thanks skalges! Here it is:yifangt@spade:~$ ls -l /bin/sh
lrwxrwxrwx 1 root root 4 Oct 11 00:03 /bin/sh -> bash Did I miss anything?
Forum: 454 Pyrosequencing 10-11-2014, 07:42 AM
Replies: 13
Views: 12,886
Posted By yifangt
Which one is the latest STLinux

I saw this list, but which one should I pick?
stlinux24-host-STLinux_deps-20100401-1.i386.rpm 01-Apr-2010 17:01 4.2K
[ ] stlinux24-host-STLinux_deps-20100427-1.i386.rpm 28-Jun-2010 14:56 4.4K...
Forum: 454 Pyrosequencing 10-10-2014, 10:18 PM
Replies: 13
Views: 10,115
Posted By yifangt
/bin/sh problem still there!

Hello, I am aware this thread is old, but I could not see any new workaround on this problem.
I am trying to install newbler 2.9.3 on Ubuntu 14.10 LTS. I did everything as emq tried according to...
Forum: Bioinformatics 02-19-2014, 08:15 AM
Replies: 2
Views: 3,228
Posted By yifangt
solution to OSError

I met same problem. Did a little bit search and found out one solution can be:
import shutilthen change this line (Line 64 at CISA.py )
os.rename('Contigs_'+final+'.fa',outfile) to ...
Forum: Bioinformatics 12-27-2013, 11:23 AM
Replies: 24
Views: 7,869
Posted By yifangt
Thanks Sven! I have sent you a couple of PM...

Thanks Sven!
I have sent you a couple of PM about the gsAssembler, as the forum does not alow PM more than 5000 char long.
locate libm.so.6
/lib/i386-linux-gnu/libm.so.6...
Forum: Bioinformatics 12-27-2013, 07:54 AM
Replies: 24
Views: 7,869
Posted By yifangt
Thanks! Under Project menu after newbler...

Thanks!

Under Project menu after newbler started, at FASTA and FASTQ reads options, on the left sight there is + icon to add sequences. After finding the fasta sequence, I clicked the + icon....
Forum: Bioinformatics 12-23-2013, 07:04 AM
Replies: 24
Views: 7,869
Posted By yifangt
Thanks Sven! I must have missed something...

Thanks Sven!
I must have missed something important.

It was /home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45
That is parrallel to the Newbler2.9 JAVA which is:...
Forum: Bioinformatics 12-20-2013, 12:37 PM
Replies: 24
Views: 7,869
Posted By yifangt
Humm, I did exactly as you suggested. When I ran:...

Humm, I did exactly as you suggested. When I ran:
/home/yt/download-software/newbler2.9/apps/gsAssembler/bin$ ./gsAssembler I had message as:
Using package java in...
Forum: Bioinformatics 12-20-2013, 08:31 AM
Replies: 24
Views: 7,869
Posted By yifangt
And I straced the errors are: ...

And I straced the errors are:
access("/etc/ld.so.preload", R_OK) = -1 ENOENT (No such file or directory)...
Forum: Bioinformatics 12-20-2013, 08:11 AM
Replies: 24
Views: 7,869
Posted By yifangt
RE: JAVA newbler2.9

Thanks Sven!
I downloaded jre1.6.0.45-x64 from Oracle, which seems to be the newest version of jre1.6.0, and installed it in
~/download-software/newbler2.9/apps/jre/jre1.6.0_45/ beside the Roche...
Forum: Bioinformatics 12-19-2013, 01:58 PM
Replies: 24
Views: 7,869
Posted By yifangt
JAVA for newbler2.9

Thanks Sklages!
There is a long list about java from the trace output, such as:
open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_30/bin/../lib/i386/jli/tls/i686/sse2/libpthread.so.0",...
Forum: Bioinformatics 12-16-2013, 11:50 AM
Replies: 24
Views: 7,869
Posted By yifangt
could not load file to projects of newbler2.9

Hi Sklages!
I could not add any data to the projects either, either .sff or .fasta/q files!!!, that I met with Newbler2.9.
You seem to be the only one who have experience to solve this problem. ...
Forum: Bioinformatics 09-27-2013, 09:41 AM
Replies: 10
Views: 4,888
Posted By yifangt
I had the exactly same problem! It seems the...

I had the exactly same problem! It seems the problem is more of -Q33 option as I tried it.
Two things here:

1) which is the wrong quality score, i.e. ASCII char when you have the -Q33 on?

2)...
Forum: Bioinformatics 08-30-2013, 09:18 AM
Replies: 4
Views: 4,410
Posted By yifangt
I am following the same question. There may be...

I am following the same question. There may be two options:
1) Redo the mapping with bowtie or bwa, what is the option to accomplish this? -k 0 does not work!

2) Filter out the SAM/BAM file. What...
Forum: Bioinformatics 07-18-2013, 03:06 PM
Replies: 136
Views: 46,487
Posted By yifangt
Yes, for Illumina Mate-pair reads, there are...

Yes, for Illumina Mate-pair reads, there are multiple scenarios that need be handled at the same time, at least the junction sequence and its reverse complement. Maybe Trim_galore can do it with...
Forum: Bioinformatics 07-18-2013, 02:31 PM
Replies: 136
Views: 46,487
Posted By yifangt
Thanks Felix, I will give it a try again. Is it...

Thanks Felix, I will give it a try again. Is it poosible to provide multiple adaptor sequences in a single line like cutadapt? It seems there is no description about this in the Trim_galore guide....
Forum: Bioinformatics 07-18-2013, 08:20 AM
Replies: 136
Views: 46,487
Posted By yifangt
trim galore error

Hello,
When I tried trim-galore (v0.3.0) for mate_pair reads (actually my first time to use it) I always had an error:
Use of uninitialized value $length_cutoff in numeric gt (>) at...
Forum: Bioinformatics 07-09-2013, 03:07 PM
Replies: 8
Views: 1,684
Posted By yifangt
OK, my 2 cents! The metrics I used includes 1)...

OK, my 2 cents!
The metrics I used includes 1) the raw reads length, 100bp each for PE, 200bp is the minimum of the two reads concatenated; but not necessary 2) the "cutoff length" of your contig...
Forum: Bioinformatics 07-09-2013, 01:32 PM
Replies: 8
Views: 1,684
Posted By yifangt
length filtering

There are bunch of scripts that can do the job if you just want to filter by length, e.g. a very short perl script.
Showing results 1 to 25 of 61

 


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