[carmeyeii]

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

[Zaag]

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.

[matan8]

How do you use the command line to map the data? I am looking for examples for that, but can't find any.

[AmitL]

If you say so, I might give it a second chance.

Thank you

[golharam]

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.

[AmitL]

Did you try it?
Its interface is very uncomfortable and it cannot be fully operated through shell scripts.

[golharam]

Just out of curiosity, why are you not using LifeScope?

[yksikaksi]

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!

Hum... it is strange. I managed to map my csfasta reads with SHRiMP2 but not BWA.

[AmitL]

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!

[yksikaksi]

Have you consider to map your csfasta reads with SHRiMP2?

[AmitL]

Alright. Thanks a lot!

[nilshomer]

How do you know it's meant for mate-pairs?

On the documentation it says:

Check out the source code "bwape.c" and search for SOLID. It uses the F3/R3 "pairing", which is mate pair.

[AmitL]

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.

[nilshomer]

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.

[AmitL]

I know the new version does not work with color-space.
Are you saying that it's true for the older versions too?