SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 19 of 19
Search took 0.00 seconds.
Search: Posts Made By: meriem
Forum: Bioinformatics 03-09-2018, 03:39 AM
Replies: 2
Views: 1,122
Posted By meriem
Thank you for your reply, My 24 contigs...

Thank you for your reply,
My 24 contigs doesn't contain any N's.
Im' doing a comparative genomic analysis of 2 strains from an extrem envirenement, I got this msg from the reviewer " In that the...
Forum: Bioinformatics 03-02-2018, 12:45 AM
Replies: 2
Views: 1,122
Posted By meriem
Question can I remove the N's in my sequence?

Hello,

I'm having a problem with mine assembly, I have a bacterial genome of 3.7bp assembled into 24 contigs, which was part of an under submission research, the reviewer gave me as a feedback...
Forum: Bioinformatics 07-30-2017, 05:18 AM
Replies: 5
Views: 1,845
Posted By meriem
hello Matt, thank you for taking time to...

hello Matt,
thank you for taking time to reply,
I'm still a bit confuse about circos, i coudn't find anywhere how to insert my sequences file.
does it use only the karyotype file without any...
Forum: Bioinformatics 07-12-2017, 11:32 AM
Replies: 0
Views: 557
Posted By meriem
Exclamation roary Error

hello, i'm trying to extract my pangenome and corgenome of my strains, i used roary and bdpt but i keep getting the same error message in both softwares i use this command : ./roary...
Forum: Bioinformatics 07-05-2017, 03:36 AM
Replies: 5
Views: 1,845
Posted By meriem
thank you very much for your reply, but how can i...

thank you very much for your reply, but how can i creat a GTF file from fasta or GBK files .. i don't know the start or the end of my contigs ?
Forum: Bioinformatics 07-04-2017, 07:25 AM
Replies: 5
Views: 1,845
Posted By meriem
circos karyotype file

hello, I'm trying to run Circos for genome comparaison of my bacterial genomes, but i can't understand how does is work, how can I make the karyotype file from my fasta and GBK files? can anyone help...
Forum: Bioinformatics 06-09-2017, 04:41 PM
Replies: 0
Views: 622
Posted By meriem
PHASTER: results interpretation

hello everyone,
can anyone help me how to interpret the result generated by PHAster, for phage detection, I'm confused do i have all these phages in my genome?
:confused::confused::confused:
Forum: Bioinformatics 06-06-2017, 08:09 AM
Replies: 0
Views: 540
Posted By meriem
HGTector for gene transfert

hello,
I want to identify if there is any horizontal gene transer in my contigs file, i found HGTector a software for horizontal gene transfer identification, I download the database but i still...
Forum: Sample Prep / Library Generation 01-27-2017, 09:39 AM
Replies: 0
Views: 909
Posted By meriem
nextera XT library préparation " pooling" ht1

hello everyone, I'm currently preparing a nextera XT library but i'm stuck in the pooling step, according to the manuel i should diluât my library in HT1 but i found 2 HT1 tubes, one with carbidge (...
Forum: Bioinformatics 12-20-2016, 03:23 AM
Replies: 1
Views: 1,177
Posted By meriem
reduce N's in my assembly

hello,
i did de novo assembly using abyss for a bacterial strain (1,6 MB), i got approximatively 600 N's according QUAST results, is it too much for the my genome length? and if so, how can i...
Forum: Bioinformatics 12-14-2016, 07:16 AM
Replies: 13
Views: 2,028
Posted By meriem
hi ali, i tried what you said but i got a very...

hi ali, i tried what you said but i got a very large picture, and according to the results i hv some contig that are the same ? :confused:
Forum: Bioinformatics 12-09-2016, 02:31 AM
Replies: 13
Views: 2,028
Posted By meriem
does it take a lot of time to do the work, cuz...

does it take a lot of time to do the work, cuz i've been running it since yesterday and still not done yet:confused:
Forum: Bioinformatics 12-08-2016, 02:28 AM
Replies: 13
Views: 2,028
Posted By meriem
yes i tried SPAdes but i didn't get satisfying...

yes i tried SPAdes but i didn't get satisfying results
Forum: Bioinformatics 12-08-2016, 02:23 AM
Replies: 13
Views: 2,028
Posted By meriem
thank you, i have already tried to run artemis...

thank you, i have already tried to run artemis but i find it hard to work with, i will try again :)
Forum: Bioinformatics 12-06-2016, 10:31 AM
Replies: 13
Views: 2,028
Posted By meriem
yes i have already annotated with quest and get...

yes i have already annotated with quest and get the following results,
bases: 3691729
tRNA: 72
CDS: 3720
rRNA: 12
repeat_region: 1
tmRNA: 1
i didn't get what you mean by orf coverage ?
Forum: Bioinformatics 12-06-2016, 09:29 AM
Replies: 13
Views: 2,028
Posted By meriem
thank you for your reply, my genome is 3,6 mb,...

thank you for your reply,
my genome is 3,6 mb, the coverage is 140.
yes i have already used quast, i think there was some fragments that were not used.
Forum: Bioinformatics 12-06-2016, 08:40 AM
Replies: 13
Views: 2,028
Posted By meriem
assembly validation

hello, i'm trying to do denovo assembly for a prokaryote strain, using different software ( Abyss, Dnastar, CLC) and i got good results, 27 contigs a hight N50, and the right size of my genome, what...
Forum: Illumina/Solexa 08-17-2016, 04:34 AM
Replies: 3
Views: 1,043
Posted By meriem
thank you for you reply, i'm doing microbial DNA...

thank you for you reply, i'm doing microbial DNA sequencing using nextera XT kit, but i'm still confused when we say 250 bp is that with adapters or only the fragments of the sample, and how can i...
Forum: Illumina/Solexa 08-16-2016, 02:47 PM
Replies: 3
Views: 1,043
Posted By meriem
Question library preparation and removing adapters

hello,
i'm new user of illumina miseq technology and i'm finding some difficulties understanding some basics.
if i select in the machine that i want to get fragments of 250 bp why do i still get ...
Showing results 1 to 19 of 19

 


All times are GMT -8. The time now is 10:43 PM.


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