[RockSOLiD]

You may find "results.tab" in your SOLiD SAGE output folder. I simply count the number of reads ID(4th column) shown in that file. If a read appears more than once, I only count it as one. Using that number divided by the total number of reads, which you may get it from the csfasta files. Hope this helps.

[aguffanti]

It's dangerous to count tags only once randomly. I postprocess the results.tab file and associate the refseq ID from a mySQL table which lnks genbank ID with RefSeq. Single RefSeqs may have many tags associated, but a tag which maps in multiple targets must be discarded, how do you know which was the correct father sequence ?

regards

Alessandro

[Pejman]

Hi
I'm a newbie! trying to find DEG though RefSeq data from SOLiD platform. I'm trying to do the alignment with the SOLiD SAGE V 1.1.0 but it just doesn't work well. I get huge amount of messages that:

"Use of uninitialized value in hash element at solid.sage.v110.pl line 1373, <F> line 1187473."

I'm using the default options, with correct input data(also tried the official sample data), but I'm not sure about the reference genome. My data is from human so I'm using the human genome from here

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/

chromFa.tar.gz - The assembly sequence in one file per chromosome.

the reference is around 4 GB already, I donno if I was supposed to use something more compact.

could anyone help me with this?


thanks
Pej

[aguffanti]

SAGE HSsreference genome format

Hi
I'm a newbie! trying to find DEG though RefSeq data from SOLiD platform. I'm trying to do the alignment with the SOLiD SAGE V 1.1.0 but it just doesn't work well. I get huge amount of messages that:

"Use of uninitialized value in hash element at solid.sage.v110.pl line 1373, <F> line 1187473."

I'm using the default options, with correct input data(also tried the official sample data), but I'm not sure about the reference genome. My data is from human so I'm using the human genome from here

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/

chromFa.tar.gz - The assembly sequence in one file per chromosome.

the reference is around 4 GB already, I donno if I was supposed to use something more compact.

could anyone help me with this?


thanks
Pej

Hi. You need the Genome reference sequence from NCBI. Check that the
chromosome headers have this format:

>gi|224384759|gb|CM000672.1| Homo sapiens chromosome 10, GRC primary reference assembly

I think this could cause your problem

Kind regards

Alessandro

[invermay]

Hi

I was wondering if someone could please comment on how the tags are generated by SOLiD SAGE? I have seen their protocol at: http://tools.invitrogen.com/content/...D_SAGE_man.pdf
where page 2 explains how the tags are generated for sequncing. What I understood and later found (in actual mappings) was that in relation to a cDNA sequence (from RefSeq for example) the tags generated by SOLiD-SAGE were reverse complemented!

Generally, one finds the tags starting with T and ending in 131 representing CATG (there are few more bases following CATG but these are not used in mappings so I am not counting those). SOLiD-SAGE software tool v1.10 maps these tags to the reverse compliment of Refseqs. We contacted local LifeTech support person and were told that the tags are just sequenced from 3' to 5' direction so shouldnt map to reverse compliments in RefSeq. This has confused me!

Has anyone tried to map the tags using any other tool (like BWA or PerM) except SOLiD-SAGE tool? If you did what was your experience with regard to orientation of the tags? I ask this as the SOLiD-SAGE tool takes whole RefSeqs fasta file and creates virtual tags from these, while with something like PerM we make the virtual tags ourselves before mapping, so creating the right tags will be the first important step before mapping. Would appreciate if someone could comment please.

Cheers