SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 17 of 17
Search took 0.00 seconds.
Search: Posts Made By: priyanka_15
Forum: Ion Torrent 12-18-2016, 08:08 PM
Replies: 0
Views: 2,691
Posted By priyanka_15
low library yield with Ion AmpliSeq Inherited disease panel

Hi All

I am facing very low yield in library when using 10ng gDNA per pool for Inherited disease panel. I have tried many things like increasing DNA amount, target amplification cycles, ensuring...
Forum: Bioinformatics 12-11-2015, 06:37 PM
Replies: 0
Views: 836
Posted By priyanka_15
Amos errors

Hello All

I have Installed Amos and trying to validate a PacBio data assembly. But whenever I run the Bank-transact command it exits saying FATAL ERROR .I/O exception..

I have attached a...
Forum: Bioinformatics 10-07-2015, 05:14 PM
Replies: 2
Views: 987
Posted By priyanka_15
Ok... then what would you suggest doing next ?

Ok... then what would you suggest doing next ?
Forum: Bioinformatics 10-06-2015, 06:16 PM
Replies: 2
Views: 987
Posted By priyanka_15
output is 0 for most .tbl file in repeatmasker output

Hello

I ran repeatmasker for my 12MB bacterial genome with rmblast and I got this result :
ile name: kib.fa
sequences: 1
total length: 12113479 bp (12113479...
Forum: Bioinformatics 10-06-2015, 10:03 AM
Replies: 33
Views: 4,305
Posted By priyanka_15
Hello ,I was able to run this with all commands...

Hello ,I was able to run this with all commands ,i did not compiled nseg properly...but I could run it then..

NOw, I have data from RepeatMAsker , the repeat library ,but it does not show any...
Forum: Bioinformatics 10-02-2015, 06:25 PM
Replies: 33
Views: 4,305
Posted By priyanka_15
did u had nseg in your path too ? I just have it...

did u had nseg in your path too ? I just have it installed the same directory as trf , is that a difference ? should I try to export nseg path too ?
Forum: Bioinformatics 10-02-2015, 05:48 PM
Replies: 33
Views: 4,305
Posted By priyanka_15
yes ,no other error message and yes I did change...

yes ,no other error message and yes I did change the name to trf.
Forum: Bioinformatics 10-02-2015, 01:22 PM
Replies: 33
Views: 4,305
Posted By priyanka_15
I did downloaded the trf from here , and also...

I did downloaded the trf from here , and also have nseg there..

as i think trf is in path right now but empty file again and ahain :(
Forum: Bioinformatics 10-02-2015, 12:42 PM
Replies: 33
Views: 4,305
Posted By priyanka_15
Hi I could run it this time but the fasta...

Hi

I could run it this time but the fasta file is empty ..
Forum: Bioinformatics 10-02-2015, 12:09 PM
Replies: 33
Views: 4,305
Posted By priyanka_15
Hello yes ,first two ran without error : ...

Hello

yes ,first two ran without error :
these are my commands for first two [./build_lmer_table -l 14 -sequence kib.fa -freq ~/Desktop/Kib15.freq
]
[/Storage_1/repeatscout/RepeatScout-1$...
Forum: Bioinformatics 10-02-2015, 11:58 AM
Replies: 33
Views: 4,305
Posted By priyanka_15
Hi, yes I did compile it by make .. I am trying...

Hi, yes I did compile it by make ..
I am trying to learn while doing this so I am using commands from the following link :
http://http://seqanswers.com/forums/showthread.php?t=5448...
Forum: Bioinformatics 10-02-2015, 11:38 AM
Replies: 33
Views: 4,305
Posted By priyanka_15
Hello I tried to do what you said ,is this...

Hello

I tried to do what you said ,is this the way ? It still is not reading the trf file :confused:
Forum: Bioinformatics 10-02-2015, 11:32 AM
Replies: 33
Views: 4,305
Posted By priyanka_15
ok , one more question should this be permanent ?...

ok , one more question should this be permanent ? because every time I close terminal it goes back to previous PATH..

I am new to this all ,perl,linux and repeatscout ; may be these are very easy...
Forum: Bioinformatics 10-02-2015, 11:17 AM
Replies: 33
Views: 4,305
Posted By priyanka_15
Tried to export PATH but still not worrking

Hi

I tried exporting the PATH But it is still not working ..PIctures attched
Forum: Bioinformatics 10-01-2015, 02:53 PM
Replies: 33
Views: 4,305
Posted By priyanka_15
Hello I did tried to put trf on my path but still...

Hello I did tried to put trf on my path but still it gives me the same error ..

CAn you suggest anything else ? I have attached a picture showing this
Forum: Bioinformatics 10-01-2015, 01:19 PM
Replies: 33
Views: 4,305
Posted By priyanka_15
Hi I am trying to run REpeatscout and when I...

Hi I am trying to run REpeatscout and when I reach to first filter stage it gives me error :
sh: 1: trf: not found
No such file or directory at ./filter-stage-1.prl line 110.
Forum: Bioinformatics 07-15-2015, 12:25 PM
Replies: 2
Views: 1,057
Posted By priyanka_15
Hi I have a similar problem but with contigs...

Hi
I have a similar problem but with contigs ,I want to extract sequences between the contigs when the contigs are aligned to a refrence..how do I extract these sequences..
Showing results 1 to 17 of 17

 


All times are GMT -8. The time now is 10:45 AM.


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