RSEQtools

[townway]

Did anyone has experience with this package?

I have problem when I use "sam2mrf" to convert my sam file from TopHat to mrf format.

$ sort -r accepted_hits.sam | sam2mrf

[dries]

hi townway,

could you give a bit more information, like a potion of your samfile?
Do you get any messages?

I worked a bit with RSEQtools, but I directly converted my export files to mrf files.

I testetd it with a (unsorted) sam file

cat test.sam | sam2mrf > test.mrf

and this worked as well.


I myself have a different question about RSEQtools:
If I calculate gene expression

cat 4-test.mrf |mrfQuantifier knownGene_composite.interval multipleOverlap > Q4.txt

In the end I get:

uc007aet.1|uc007aeu.1 0.022290
uc007aev.1 0.012031
uc007aew.1|uc007aex.1 0.000000
uc007aey.1|uc007aez.1|uc007afa.1|uc007afb.1|uc007afc.1 0.079886
uc007afd.1|uc007afe.1|uc007aff.1 126.692540
uc007afg.1|uc007afh.1 32.264091
uc007afi.1|uc007afj.1 8.446543
uc007afk.1|uc007afl.1 1.554995
uc007afm.1|uc007afn.1 22.757426
uc007afo.1|uc007afp.1|uc007afq.1 0.010738
uc007afr.1|uc007afs.1|uc007aft.1|uc007afu.1 3.733889
uc007afv.1 0.259307
uc007afw.1|uc007afx.1|uc007afy.1|uc007afz.1|uc007aga.1 0.000000
uc007agb.1|uc007agc.1|uc007agd.1 7.503322

Does anyone know how to link the values to actual genenames?

Best,
David

[townway]

you might go to ucsc table browser to select the right categories and pull the annotations you want.

BTW, what aligner you use?

[dries]

Hi,

yes, I pulled a table which has the genenames included but (although I guess it's pretty basic) I don't know how to merge these two lists to get one with only genenames an expr. values.

#mm9.knownIsoforms.clusterId	mm9.knownIsoforms.transcript	mm9.kgXref.geneSymbol
1	uc007aeu.1	Xkr4
1	uc007aet.1	mKIAA1889
2	uc007aev.1	AK149000
3	uc007aew.1	Rp1
3	uc007aex.1	Rp1h
4	uc007aey.1	Sox17
4	uc007afc.1	Sox17
4	uc007afb.1	Sox17
4	uc007afa.1	Sox17
4	uc007aez.1	Sox17
5	uc007afd.1	Mrpl15
5	uc007aff.1	Mrpl15
5	uc007afe.1	Mrpl15
6	uc007afg.1	Lypla1

We get our data already ELAND aligned.

[Aman Mahajan]

Query

I used SOAPaligner to align my reads and converted output to SAM format using soap2sam.pl.

I want to run RSEQtools on my SAM file. I have compiled the software and set the environment variables. Having trouble with sam2mrf utility in it. Any idea?

Thanks.

[bharati]

I am unable to use sam2mrf provided by prebuilt binaries of RSEQtools, can anybody pls help?
The command I tried was "sort -r file.sam | sam2mrf > file.mrf"
as specified in the manual for the alignment file generated by tophat but it didnt work.

please reply soon.

[zjrouc]

Did anyone has experience with this package?

I have problem when I use "sam2mrf" to convert my sam file from TopHat to mrf format.

$ sort -r accepted_hits.sam | sam2mrf

Hi, i met the similar problem, did you solve this? Sam2mrf doesn't work on my paired-end alignment output. It was always stuck with some alignment in SAM and i dont know why. i sorted SAM file using samtools sort -n and sort -r, both doesn't work. anyone can help me about this?