SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 36
Search took 0.02 seconds.
Search: Posts Made By: Giffredo
Forum: Bioinformatics 08-29-2016, 02:07 AM
Replies: 14
Views: 9,362
Posted By Giffredo
now I receive this error: ValueError:...

now I receive this error:

ValueError: Specified alphabet DNAAlphabet() clashes with that determined from the file, Alphabet()

I think I have not Bio.Alphabet...
Forum: Bioinformatics 08-29-2016, 01:46 AM
Replies: 14
Views: 9,362
Posted By Giffredo
This is the head: $ head fileA.gbk LOCUS ...

This is the head:

$ head fileA.gbk
LOCUS DG_Contig_04
DEFINITION seqnum=1;seqlen=498669;seqhdr="DG_final_Contig_04";version=Prodigal.v2.50;run_type=Single;model="Ab...
Forum: Bioinformatics 08-29-2016, 01:35 AM
Replies: 14
Views: 9,362
Posted By Giffredo
Hi, the python script doesn't work on my...

Hi,
the python script doesn't work on my genbank files.

"ValueError: Need a Nucleotide or Protein alphabet"

Anyway.. If I have several genbank files can I use the function:
in_genbank =...
Forum: Bioinformatics 02-11-2015, 01:26 AM
Replies: 2
Views: 2,029
Posted By Giffredo
Yes, thank you! it was a problem linked with...

Yes, thank you!
it was a problem linked with the lack of memory. Now it works well!
Forum: Bioinformatics 02-10-2015, 02:07 AM
Replies: 2
Views: 2,029
Posted By Giffredo
MIRA denovo assembly

Hi,

I have a problem with MIRA 4 assembly denovo using reads in fastq format come from ion Torrent technology.

my manifest file is:

project = pDG2
job = denovo
readgroup = lab
data =...
Forum: Bioinformatics 12-01-2014, 12:52 AM
Replies: 0
Views: 1,549
Posted By Giffredo
merge .biom files

Hi,

I would like to ask you if it is possible to merge .biom file.
Maybe it is not possible directly but starting from the bam files?

I tried the code
merge_otu_tables.py -i...
Forum: Bioinformatics 04-17-2014, 12:44 AM
Replies: 24
Views: 13,396
Posted By Giffredo
When I insert this code pysamstats -f x.fas...

When I insert this code
pysamstats -f x.fas --type variation_strand mapq_strand x.sorted.bam > stat_pyout.txt&

Py gives me this error:
pysamstats: error: missing file operand

What it means?...
Forum: Bioinformatics 04-15-2014, 02:33 AM
Replies: 24
Views: 13,396
Posted By Giffredo
Ok, I understood... In which way I could...

Ok, I understood... In which way I could discriminate the splicing site osing pysamstat output?
I would see the deletion sites present on my reads and not present on the references and I would...
Forum: Bioinformatics 04-10-2014, 01:12 AM
Replies: 24
Views: 13,396
Posted By Giffredo
I have not any idea.. I cannot install anything...

I have not any idea.. I cannot install anything in this Lab. there is an expert for this and he told me that is not possible. I guess it is a problem about compatibility..
Forum: Bioinformatics 04-10-2014, 12:44 AM
Replies: 24
Views: 13,396
Posted By Giffredo
Unfortunately I cannot install pysamstat...

Unfortunately I cannot install pysamstat package..
So, Is it possible to reach the same results using GATK for you?.. looking at the tutorial I think it cannot discriminate the variation in one...
Forum: Bioinformatics 03-26-2014, 04:06 AM
Replies: 24
Views: 13,396
Posted By Giffredo
I am very interested on this discussion.. Can...

I am very interested on this discussion..
Can Pysamstats give me the difference between reds (forward or reverse)?

I need a table with these informations:
...
Forum: Bioinformatics 03-12-2014, 07:03 AM
Replies: 0
Views: 766
Posted By Giffredo
VarScan output

I d like to count the reads for each position (keep the information about F or R strand) on my chromosome.
I tried with mpileup but it give me results not easily to manage for a statistical work....
Forum: Bioinformatics 03-12-2014, 06:47 AM
Replies: 20
Views: 5,268
Posted By Giffredo
Ok, I think it is a good idea.. Anyway thank...

Ok, I think it is a good idea..

Anyway thank dpryan for all your suggests. I appreciated them so much :)
Forum: Bioinformatics 03-12-2014, 04:32 AM
Replies: 20
Views: 5,268
Posted By Giffredo
before starting to make a script, I tried...

before starting to make a script, I tried VarScan..

Reading input from Pileup_merge.pileup (VARSCAN)
chrM 1 G 4 3 G:3:1:21:1:0:3:0
chrM 2 G 4 4 ...
Forum: Bioinformatics 03-11-2014, 03:25 AM
Replies: 20
Views: 5,268
Posted By Giffredo
ok I understood the output that mpileup give me. ...

ok I understood the output that mpileup give me.

Now I think that should exist a "script" to translate the output.. I mean: if I have ....,. in the output it means I have 6 reads in total in that...
Forum: Bioinformatics 03-10-2014, 12:10 AM
Replies: 20
Views: 5,268
Posted By Giffredo
OK.. but I have still some doubts: I know "," is...

OK.. but I have still some doubts: I know "," is a base call and for this reason I don t understand why I have more than one "," for only one base in one position... :confused:

..and what is...
Forum: Bioinformatics 03-07-2014, 07:20 AM
Replies: 20
Views: 5,268
Posted By Giffredo
I think it is not... I expected something like...

I think it is not...
I expected something like this but with the right symbol in the right positions in order to have the possibility to translate and understand them!
where are the read bases?...
Forum: Bioinformatics 03-07-2014, 05:14 AM
Replies: 20
Views: 5,268
Posted By Giffredo
chrM 136 A 6 ,,,,,, 896774 ...

chrM 136 A 6 ,,,,,, 896774
chrM 137 A 6 ,,,,,, ?=@===
chrM 138 A 6 ,,,,,, ?=<=8<
chrM 139 C 6 ,,,,,, 887801
chrM ...
Forum: Bioinformatics 03-07-2014, 04:58 AM
Replies: 20
Views: 5,268
Posted By Giffredo
Ok thanks!!! I will try. About & I know.. I put...

Ok thanks!!! I will try.
About & I know.. I put it because of force of habit.. ...
Forum: Bioinformatics 03-07-2014, 03:29 AM
Replies: 20
Views: 5,268
Posted By Giffredo
So, are you telling me that the output from ...

So, are you telling me that the output from
samtools mpileup -f .fas .sorted.bam
is a .txt?

.. then if I use..

samtools mpileup -f .fas .sorted.bam | tee teeoutput.txt&

...I ll reach...
Forum: Bioinformatics 03-06-2014, 05:31 AM
Replies: 20
Views: 5,268
Posted By Giffredo
samtools mpileup -f .fas .sorted.bam > .bcf |...

samtools mpileup -f .fas .sorted.bam > .bcf | bcftools view > .vcf&


Just now I have used

samtools mpileup -f .fas .sorted.bam | tee teeoutput.bcf&

This "artefact" maybe works.. :)
Forum: Bioinformatics 03-05-2014, 11:17 PM
Replies: 20
Views: 5,268
Posted By Giffredo
I have the same problem but I have not "seen" yet...

I have the same problem but I have not "seen" yet ...

i want to use mpileup without -u and -g options but all the command line used did not work..
Forum: Bioinformatics 02-28-2014, 12:18 AM
Replies: 24
Views: 13,396
Posted By Giffredo
OK.. so which is the difference between z and w?

OK.. so which is the difference between z and w?
Forum: Bioinformatics 02-27-2014, 11:43 PM
Replies: 8
Views: 2,166
Posted By Giffredo
Thank Rick and Ryan very much! I read about...

Thank Rick and Ryan very much!

I read about STAR but I have to stay with Tophat (Anyway by now it is a "friend" for me :p)

the function of --read-edit-dist parameter is not actually clear........
Forum: Bioinformatics 02-27-2014, 06:42 AM
Replies: 8
Views: 2,166
Posted By Giffredo
Are you sure? i read this: "The software is...

Are you sure?

i read this: "The software is optimized for reads 75bp or longer."
Showing results 1 to 25 of 36

 


All times are GMT -8. The time now is 12:29 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO