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Forum: Pacific Biosciences 07-30-2015, 08:14 PM
Replies: 4
Views: 1,261
Posted By gerald2545
Thanks for your replies.... you are right, I...

Thanks for your replies....
you are right, I knew this documentation, but it seems I didn't spend enough time reading it...I now find the useful web methods "Scan for New Input Metadata Function"...
Forum: Pacific Biosciences 07-29-2015, 01:16 AM
Replies: 4
Views: 1,261
Posted By gerald2545
Automate SMRCT Cells import in SMRT portal

Hi all,
we have installed a PacBio RSII few month ago in our core facility, and SMRT poral is working fine (2.3.0). Now we would like to setup SMRT portal to automate SMRT Cells import and give the...
Forum: Bioinformatics 08-24-2013, 12:12 PM
Replies: 649
Views: 169,925
Posted By gerald2545
jute a follow-up, the same file took 1500 minutes...

jute a follow-up, the same file took 1500 minutes to sort with -k3,3 parameter

gerald
Forum: Bioinformatics 08-23-2013, 06:28 AM
Replies: 649
Views: 169,925
Posted By gerald2545
Thank you Felix for your time, but don't forget :...

Thank you Felix for your time, but don't forget : you are on holidays ;)

Gérald
Forum: Bioinformatics 08-23-2013, 03:23 AM
Replies: 649
Views: 169,925
Posted By gerald2545
bismark_methylation_extraction sort

Hi all,
I have a question regarding sorting the methXtractor.temp files
I may not have enough background using this tool, but I wonder why the sort command in bismark2bedGraph script

has the...
Forum: Bioinformatics 08-22-2013, 11:46 PM
Replies: 136
Views: 41,031
Posted By gerald2545
Hi Felix, no worry about the late reply, I knew...

Hi Felix,
no worry about the late reply, I knew that you were on holiday.

Thank you for the information. Maybe for paired-ends run, the following sentence could be omitted in the report : ...
Forum: Bioinformatics 08-19-2013, 12:55 AM
Replies: 136
Views: 41,031
Posted By gerald2545
just tested with 0.3.1 version, we notice the...

just tested with 0.3.1 version, we notice the same behaviour

Best regards

Gérald
Forum: Bioinformatics 08-19-2013, 12:28 AM
Replies: 136
Views: 41,031
Posted By gerald2545
Hi all, we noticed something strange in...

Hi all,
we noticed something strange in TrimGalore! (0.2.8) result file, for a WGBS 2x101 paired-ends run :




It seems that 0 reads were removed for R1 due to length, 0 reads were removed...
Forum: Illumina/Solexa 11-22-2011, 12:40 AM
Replies: 14
Views: 7,019
Posted By gerald2545
it is due to the the EWF (Enhanced Write Filter)...

it is due to the the EWF (Enhanced Write Filter) activated in windows : you can do evertything you want in the C: drive (installing software, write files...), but by default, when you reboot your...
Forum: Bioinformatics 12-04-2010, 09:11 PM
Replies: 3
Views: 4,768
Posted By gerald2545
Hello did you try "samtools reheader"? Never...

Hello
did you try "samtools reheader"?
Never used, but seems to do what you want

Gerald
Forum: Bioinformatics 12-01-2010, 11:43 AM
Replies: 6
Views: 3,204
Posted By gerald2545
you can also use the samtools view -X option...

you can also use the samtools view -X option which transforms the flag to a string, human readable.
samtools view -? for details

Gerald
Forum: Bioinformatics 11-30-2010, 11:11 AM
Replies: 10
Views: 6,018
Posted By gerald2545
generate missing qseq files with Bustard

rerun setupBclToQseq.py
go into your output directory
edit Makefile.config file
from the line : lanes := s_1 s_2 s_3 s_4 s_5 s_6 s_7 s_8, delete the lanes for which you don't want the qseq and...
Forum: 454 Pyrosequencing 05-18-2009, 12:00 AM
Replies: 12
Views: 4,838
Posted By gerald2545
Thank you for your message, I found the...

Thank you for your message, I found the information in the documentation on page 69 about generating the sff files for failed reads. I also didn't find a way to extract them, even in the history.xml...
Forum: 454 Pyrosequencing 04-29-2009, 01:47 AM
Replies: 12
Views: 4,838
Posted By gerald2545
could you please attach your template xml file...

could you please attach your template xml file please?
if you generate the filterOnly xml file and execute runAnalysusFilter with this file, do you have the same error?

could you insert the...
Forum: 454 Pyrosequencing 04-28-2009, 08:37 AM
Replies: 12
Views: 4,838
Posted By gerald2545
OK....thank you for your precious help.

OK....thank you for your precious help.
Forum: 454 Pyrosequencing 04-28-2009, 08:04 AM
Replies: 12
Views: 4,838
Posted By gerald2545
Do you have errors in gsRunProcessor_err.log or...

Do you have errors in gsRunProcessor_err.log or gsRunProcessor.log files, in the D_ repository?

could you please attach you xml file?


OK...didn't find it in the manual. I didn't find the...
Forum: 454 Pyrosequencing 04-23-2009, 05:41 AM
Replies: 12
Views: 4,838
Posted By gerald2545
You gave me the right way to get untrimmed...

You gave me the right way to get untrimmed sequances for the reads whiche passed all quality filters, it helped us, but what I really wanted to do is generate the reads with less stringent filters.
...
Forum: 454 Pyrosequencing 04-21-2009, 01:08 AM
Replies: 12
Views: 4,838
Posted By gerald2545
Thank you for your reply!!! Discussing with my...

Thank you for your reply!!!
Discussing with my colleagues (I'm a computer scientist) : they have done the titration.
For region 1, it seems that the result was not so good, they had to incorporate...
Forum: 454 Pyrosequencing 04-16-2009, 10:57 PM
Replies: 34
Views: 14,523
Posted By gerald2545
Hi, we run only few project on our 454...

Hi,
we run only few project on our 454 (titanium only) and we were surprised about the amount of filtered reads and the length of the high quality reads. could you please tell me (if possible) the...
Forum: 454 Pyrosequencing 04-15-2009, 09:38 AM
Replies: 12
Views: 4,838
Posted By gerald2545
getting reads not filtered?

Hi all,
do you know if there is a way to get the sequences before all the filters are applied?

I know that I can modify the stringency of quality filtering for TrimBack Valley and quality score...
Forum: Introductions 11-13-2008, 01:29 AM
Replies: 0
Views: 1,307
Posted By gerald2545
Hi from Toulouse

I work in a core facility in Toulouse - INRA and we received a Roche 454 with our first run done last week.
I'm interested in learning more about this machine, data analysis.....
Hope I could...
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