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Old 04-11-2013, 06:07 AM   #1
zisis86
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Location: Poznan,Poland

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Default searching tools and informations about 4C seq analysis

Hi,
Do we have any news about 4C seq analysis tools?
I am trying to use one tool with the name 4cseqpipe available here http://compgenomics.weizmann.ac.il/tanay/?page_id=367.
Does anyone used this for a data set?
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Old 09-01-2015, 12:00 AM   #2
shruti
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Hi,

I am also using 4cseqpipe but getting the message
Mapper will quit now. Please reduce the value for "min_precision_for_weight" setting and run again the program.
Also beware that you might experience slow run-times with low quality reads.
To improve run-times consider lowering down the precision by reducing the value of "max_mismatches".

But there is no option to change the values of these parameters.
Anyone has any idea?

thanks
shruti
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Old 09-01-2015, 11:07 AM   #3
ranting_swede
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Hey Shruti,

I'm having the same issue going into mapping "Mapper will quit now..."

I'll let you know if I come up with anything, but does anyone else have any input? I don't see this issue with the example data but I'm not sure if it's data quality or a pipeline issue yet. I'm trying to just trim and map with bowtie myself just as a sanity check. The read structure and fastqc look okay at least...
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Old 09-04-2015, 08:16 AM   #4
ranting_swede
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So for me the issue was with the quality score encoding. Try using "-convert_qual" when running the first stage of the pipeline. Weird that the error message was about mapping precision, but I'm glad it's fixed at least.

As far as I can tell "min_precision_for_weight" is hardcoded in the C++ mapper.
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Old 09-08-2015, 11:58 PM   #5
shruti
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Thanks ranting_swede,

will try and let you know. I guess I misunderstood the function of the parameter "-convert_qual" before.
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Old 09-14-2015, 02:06 AM   #6
shruti
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Hi...
just to report.. my problem was solved by using the parameter -convert_qual 1
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Old 01-05-2016, 07:31 AM   #7
shruti
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Hi,

For some of my samples while running 4cseqpipe I am running into the following error:

Error in approx(bd$start, uni_cut_3, n = length(bd$start)) :
need at least two non-NA values to interpolate
Execution halted

Anyone has an idea what to do? or check?
Thanks

shruti
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