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Search: Posts Made By: arthur.yxt
Forum: Bioinformatics 06-11-2013, 02:32 PM
Replies: 0
Views: 1,700
Posted By arthur.yxt
python script modification of LSC0.2.4 ?

It's really really great news that LSC now takes BWA into usage in the current version of 0.2.4. It took me one whole day only to find out that the master script "runLSC.py" might need some changes...
Forum: Bioinformatics 12-27-2009, 07:23 AM
Replies: 0
Views: 7,109
Posted By arthur.yxt
Bowie12Beta mapping direction restriction or bug?

Dear all, I was trying to map 76nt reads using Bowtie. I wanted to use the "seed" feature to avoid trimming off the adapter sequence.

1) this is the sequence that I trimmed off the last "4nt"...
Forum: Bioinformatics 10-20-2009, 04:59 AM
Replies: 30
Views: 13,526
Posted By arthur.yxt
i guess that exon only belong to one mRNA, but a...

i guess that exon only belong to one mRNA, but a mRNA may have multiple transcripts
Forum: Bioinformatics 10-16-2009, 01:47 AM
Replies: 19
Views: 6,884
Posted By arthur.yxt
well i don't know. In fact I find it kinda...

well i don't know. In fact I find it kinda strange that the flag=19 alignment holds mismatch=3, but flag=83 alignment holds mismatch=1. Can a sequence map to one location but with different...
Forum: Bioinformatics 10-16-2009, 12:59 AM
Replies: 1
Views: 1,393
Posted By arthur.yxt
for reads length < 20bp, try only report only one...

for reads length < 20bp, try only report only one random alignment, this would help.
BTW, the latest version of bowtie seems to be 0.11.3?
Forum: Bioinformatics 10-16-2009, 12:52 AM
Replies: 19
Views: 6,884
Posted By arthur.yxt
to pengchy

##these three lines confused me that why the last two lines are different, because they are the same reads that hit on the same location?
FC42DB6AAXX:3:91:1346:410#0 163 scaffold507 50287 255 75M =...
Forum: Bioinformatics 10-15-2009, 05:04 PM
Replies: 30
Views: 13,526
Posted By arthur.yxt
I just found something. I build cufflinks myself...

I just found something. I build cufflinks myself and rerun the command like: cufflinks -m 50 -I 1000000 -p 4 -G sample.sam sample.gft [wrongly by mistake]. Error came:
"Error parsing strand (=) from...
Forum: Bioinformatics 10-15-2009, 03:17 PM
Replies: 6
Views: 3,596
Posted By arthur.yxt
I added -G but still get no RPKM. Any...

I added -G but still get no RPKM. Any suggestions please? this is my command:

tophat -r 50 --mate-std-dev 100 -a 5 -i 50 -I 1000000 -p 4 --solexa1.3-qual --coverage-search --fill-gaps...
Forum: Bioinformatics 10-15-2009, 03:13 PM
Replies: 30
Views: 13,526
Posted By arthur.yxt
I also have problem with this tag. I tried to add...

I also have problem with this tag. I tried to add "XS:A:" to the end of each line in sam and I tried to replace the original field "XA:i:~" with "XS:A:", neither worked. cufflink simply prompt...
Forum: Bioinformatics 10-15-2009, 03:19 AM
Replies: 15
Views: 5,519
Posted By arthur.yxt
SAM result format required in cufflinks

Hi all,

Tophat is a great, but it seems not working so well with Cufflinks. As Cufflinks require the .SAM result containing the "XS:A:" field and Tophat don't provide this, I will have to add...
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