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Forum: Bioinformatics 12-06-2010, 07:26 AM
Replies: 10
Views: 3,283
Posted By glacierbird
sam error msg here.

sam error msg here.
Forum: Bioinformatics 08-03-2010, 07:44 AM
Replies: 2
Views: 2,434
Posted By glacierbird
^@ in .combined.gtf from cuffcompare v0.8.4

Hi,

after cufflinks generates tnp1/transcripts.gtf tmp2/transcripts.gtf (attached: tmp_gtf.zip)

I run cuffcompare (attachted: combined_gtf.zip) to generate a .combined.gtf from both of these...
Forum: Bioinformatics 07-19-2010, 07:45 AM
Replies: 10
Views: 2,916
Posted By glacierbird
Hi, I also got the same error msg, even...

Hi,

I also got the same error msg, even without a reference.

Did you find the explanation?
Forum: Bioinformatics 07-14-2010, 04:28 AM
Replies: 13
Views: 8,924
Posted By glacierbird
Hi, what do you mean of query...

Hi,




what do you mean of query length? I suppose query length = read length. If so, every read length=72

From this CIGAR "36M92N36M473N536870911M"
36M+36M=72, that's why I want to...
Forum: Bioinformatics 07-13-2010, 12:15 AM
Replies: 13
Views: 8,924
Posted By glacierbird
I have tried to delete 536870911M But it...

I have tried to delete
536870911M

But it still doesn't work.

I have no clue where is these 536970911 from.
Forum: Bioinformatics 07-13-2010, 12:14 AM
Replies: 13
Views: 8,924
Posted By glacierbird
I have the same problem with CIGAR by using...

I have the same problem with CIGAR by using TOPHAT

tophat -p 4 --solexa1.3-quals -o directory index fastq

there are several lines cause error msg when I want to convert .sam to .bam
...
Forum: Bioinformatics 06-29-2010, 01:58 AM
Replies: 2
Views: 6,677
Posted By glacierbird
I think the solution could be: reformat the raw...

I think the solution could be:
reformat the raw .fastq file.

Maybe, somewhere is not Tab, but space.

then, 536870911M
will not occur.
Forum: Bioinformatics 06-29-2010, 01:29 AM
Replies: 2
Views: 6,677
Posted By glacierbird
I think the problem is caused by: ...

I think the problem is caused by:

36M92N36M473N536870911M

But, I don't know how could it occur?
Forum: Bioinformatics 06-29-2010, 01:13 AM
Replies: 292
Views: 158,636
Posted By glacierbird
Hi Li, I parse .sam with sequence, but samtools...

Hi Li,
I parse .sam with sequence, but samtools view still gave such error msg. Could you please take a look of the post:
http://seqanswers.com/forums/showthread.php?p=21003#post21003

Thanks.
Forum: Bioinformatics 06-29-2010, 01:09 AM
Replies: 2
Views: 6,677
Posted By glacierbird
Question samtools view error: CIGAR and sequence length are inconsistent (tophat/bowtie)

Hi,
When I try to use "samtools view" to creat .bam file from .sam, I get these error msg. The .sam file is created by mapping raw illumina reads with tophat.

samtools view -bS -t index.fa.fai...
Forum: Bioinformatics 02-06-2010, 05:25 AM
Replies: 2
Views: 3,749
Posted By glacierbird
http://www.ncbi.nlm.nih.gov/sra/

http://www.ncbi.nlm.nih.gov/sra/
Forum: Bioinformatics 02-03-2010, 12:50 PM
Replies: 2
Views: 3,749
Posted By glacierbird
ok, starting to collect info from this forum...

ok, starting to collect info from this forum first:

# data
http://www.ebi.ac.uk/embl/Documentation/ENA-Reads.html

http://www.bioinformatics.bbsrc.ac.uk/training.html#seqmonk

# tips from...
Forum: Bioinformatics 02-03-2010, 12:43 PM
Replies: 13
Views: 4,513
Posted By glacierbird
this post is very helpful for me as well! ...

this post is very helpful for me as well!

Thanks.
Forum: Bioinformatics 02-03-2010, 12:35 PM
Replies: 2
Views: 3,749
Posted By glacierbird
Exclamation real world 454 sequencing data analysis examples?!

Hi All,

I am interested in 454 data analysis, and plan to teach myself.

Could anybody kindly provides some data files and some potential problems that need to be solved, so that I can explore...
Forum: 454 Pyrosequencing 02-03-2010, 12:31 PM
Replies: 0
Views: 1,713
Posted By glacierbird
Thumbs up real world 454 sequencing data analysis examples?!

Hi All,

I am interested in 454 data analysis, and plan to teach myself.

Could anybody kindly provides some data files and some potential problems that need to be solved, so that I can explore...
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