Hi!
I'm analyzing a "second-hand" dataset generated using SOLiD 4. It is a transcriptome mate pair library that is 52 x 37 nt, and I cannot for the sake of me find the protocol that was used to generate those specific read lengths. I have F3 and R3 reads, so I am assuming it is a circularization protocol, but I do not know what the size selection parameters were, or how the circles were cut to produce the final fragments. This info would be very valuable for a more accurate mapping.
Any knowledge would be greatly appreciated!
Thanks a lot,
Carmen
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From the manual (buildup of the manual is as horrible as the GUI):
1. Create a text file with one command per line. For example:
cd proj1
cd run2
set workflow analysis.pln
add xsq xsqfile
set reference hg19
run
ls
exit
2. Save the file, for example as proj1script.
3. Then run with this command:
lscope.sh -u user -w password < proj1script
Note: This example does not include the commands necessary to step up a new analysis.
See page 78 of the Command shell user guide, there are several other/easier ways if you have standard pipelines.
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How do you use the command line to map the data? I am looking for examples for that, but can't find any.
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I agree. I only use LifeScope to map data, and I use the command-line interface. The GUI is horrible. Once I have the BAM files I do the rest of my processing outside of LifeScope.
I ask because I keep hearing LifeScope does a better job mapping reads than other tools. I haven't tried others myself though.
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Did you try it?
Its interface is very uncomfortable and it cannot be fully operated through shell scripts.
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Originally posted by AmitL View PostYes.
Shrimp2 collapses because of non-existing input problems. I have checked the input manually and it was ok. It works with all other tools.
I preferred not to deal with such a buggy tool.
But thanks!
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Yes.
Shrimp2 collapses because of non-existing input problems. I have checked the input manually and it was ok. It works with all other tools.
I preferred not to deal with such a buggy tool.
But thanks!
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How do you know it's meant for mate-pairs?
On the documentation it says:
Generate alignments in the SAM format given paired-end reads.
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The new version does not work with color space. The older version works with mate pairs and color space, but not paired end and color space.
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I know the new version does not work with color-space.
Are you saying that it's true for the older versions too?
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