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Forum: Academic/Non-Profit Jobs 03-26-2020, 02:41 AM
Replies: 1
Views: 1,270
Posted By afadda
Experienced bioinformatician job in Qatar

A 2-year job opportunity is available in Sidra/Qatar on a grant-funded position. The project requires skills in bioinformatics in general, NGS data analysis, both genomic and transcriptomic data,...
Forum: Bioinformatics 06-21-2017, 01:16 AM
Replies: 3
Views: 1,636
Posted By afadda
hi evakoe, which command did you use? cuz...

hi evakoe,

which command did you use? cuz i'm trying to do the same but it's not working.
i'm using this:
run-bwamem -o NA12878-hs38 -t 20 -H -s...
Forum: Genomic Resequencing 07-31-2013, 07:53 AM
Replies: 1
Views: 1,753
Posted By afadda
gene copy number -k parameter

hi,
I have 3 questions on the same problem:
I'm aligning reference DNAseq (illumina) to itself. I plot the gene coverage histogram and try to calculate the gene copy number assuming the peak...
Forum: Bioinformatics 08-10-2012, 04:54 AM
Replies: 11
Views: 8,768
Posted By afadda
you're absolutely right. it's a programming...

you're absolutely right. it's a programming mistake on my side when i was trimming the reads, so that the read in the error message had different length for quality.
thanks for trouble shooting!...
Forum: Bioinformatics 08-10-2012, 04:33 AM
Replies: 11
Views: 8,768
Posted By afadda
yes. message is: Too few quality values for...

yes. message is:
Too few quality values for read: HWI-ST1146:66:C0YHCACXX:7:1101:8166:5424 1:N:0:ACTTGA
are you sure this is a FASTQ-int file?

my command line is:
bowtie -S -a --best --strata...
Forum: Bioinformatics 08-10-2012, 04:02 AM
Replies: 11
Views: 8,768
Posted By afadda
what i have is this ...

what i have is this

@HWI-ST1146:66:C0YHCACXX:7:1101:2909:2074 1:N:0:ATCACG
CCACTAGCTTTCCTGGCAC
+
JJEHIJIIJJJHEHFHFFF

so the number of letters is the same for the read and the quality. I'm...
Forum: Bioinformatics 08-09-2012, 08:27 AM
Replies: 11
Views: 8,768
Posted By afadda
maubp, what does that mean? I have the same...

maubp, what does that mean? I have the same problem as kz26. Help please!
Forum: General 01-04-2012, 03:15 AM
Replies: 1
Views: 1,705
Posted By afadda
Bowtie reporting on number of reads

Hi,
is there away to have bowtie report the summary of reads processed and aligned to a file?
thanks,
Forum: Bioinformatics 02-11-2011, 06:03 AM
Replies: 39
Views: 20,227
Posted By afadda
thanks Simon. it's working now!

thanks Simon. it's working now!
Forum: Bioinformatics 02-10-2011, 08:35 AM
Replies: 39
Views: 20,227
Posted By afadda
> head(table) WT1 WT2 T ...

> head(table)
WT1 WT2 T
Tb927.1.10 0 0 0
Tb927.1.30 0 0 0
Tb927.1.40 0 0 0
Tb927.1.110 2260 2914 4825
Tb927.1.270 214 278 359
Tb927.1.280 205...
Forum: Bioinformatics 02-10-2011, 06:51 AM
Replies: 39
Views: 20,227
Posted By afadda
how about this error > cds= newCountDataSet(...

how about this error

> cds= newCountDataSet( table, conds )
Error in if (any(round(countData) != countData)) stop("The countData is not integer.") :
missing value where TRUE/FALSE needed

...
Forum: Bioinformatics 02-09-2011, 09:17 AM
Replies: 39
Views: 20,227
Posted By afadda
ok. I'm ignorant in R... I don't seem to be...

ok. I'm ignorant in R...
I don't seem to be able to get the newCountDataSet to work. I get this error:
Error in round(countData) : Non-numeric argument to mathematical function
I checked, and non...
Forum: Bioinformatics 02-09-2011, 04:55 AM
Replies: 39
Views: 20,227
Posted By afadda
Hi, I have installed DESeq and all seems right:...

Hi,
I have installed DESeq and all seems right:

> biocLite("DESeq")
Using R version 2.11.1, biocinstall version 2.6.9.
Installing Bioconductor version 2.6 packages:
[1] "DESeq"
Please wait......
Forum: Bioinformatics 06-18-2010, 05:05 AM
Replies: 514
Views: 212,529
Posted By afadda
sorry!! I actually meant samtools view. perhaps...

sorry!! I actually meant samtools view. perhaps this is not the right string for my problem.
thanks
Forum: Bioinformatics 06-18-2010, 04:53 AM
Replies: 514
Views: 212,529
Posted By afadda
hi. i get segmentation fault only when I run...

hi. i get segmentation fault only when I run bwotie view on a certain data. it always stops at the same genome coordinates, whether it's in one big file with all chromosomes in, or just a file of...
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