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Search: Posts Made By: urchgene
Forum: Bioinformatics 06-21-2011, 04:44 AM
Replies: 12
Views: 5,837
Posted By urchgene
Hi all, I am running denovo assembly with...

Hi all,

I am running denovo assembly with velvet color space build and when i run velveth_de, it terminates halfway before it writes the ./Roadmap file. I have no idea what the problem is and i am...
Forum: Bioinformatics 04-19-2011, 05:52 AM
Replies: 16
Views: 5,210
Posted By urchgene
Hi everyone.................I am trying to do...

Hi everyone.................I am trying to do paired end mapping using SHRiMP but it requires that i have both the + orientation and - orientation of these reads following each other simultaneously...
Forum: Bioinformatics 11-18-2010, 10:17 AM
Replies: 47
Views: 24,483
Posted By urchgene
i have been encountering problems in this run and...

i have been encountering problems in this run and never got it completed for once.

This is my command................it is a single fragment solid run

tophat -C -p 8 -r 100 -I 1200...
Forum: Bioinformatics 11-11-2010, 01:48 AM
Replies: 38
Views: 9,370
Posted By urchgene
@ caddymob...........................not sure i...

@ caddymob...........................not sure i understood your question but

i copied and pasted the @HD VN:1.0 SO:coordinate into a txt file header.txt as you advised.

but since that did...
Forum: Bioinformatics 11-11-2010, 12:34 AM
Replies: 38
Views: 9,370
Posted By urchgene
@caddymob .......................seems to be...

@caddymob .......................seems to be there is a problem with this file stub_header.sam

samtools view -H stub_header.sam > header.txt

error:
[bam_header_read] EOF marker is absent....
Forum: Bioinformatics 11-11-2010, 12:25 AM
Replies: 38
Views: 9,370
Posted By urchgene
@caddymob...................thanks, i will try...

@caddymob...................thanks, i will try that now.
Forum: Bioinformatics 11-10-2010, 11:57 PM
Replies: 38
Views: 9,370
Posted By urchgene
i tried to see what is happening and why the...

i tried to see what is happening and why the output files are empty. picard-tools runs.

For example i try to convert bowtie aligned reads from sam to fastq

java -Xmx2g -jar SortSam.jar...
Forum: Bioinformatics 11-10-2010, 11:31 PM
Replies: 38
Views: 9,370
Posted By urchgene
@adarob..........i am using tophat 1.1.2 as you...

@adarob..........i am using tophat 1.1.2 as you can see below but i still get the wrong header which gives the error.....

which tophat...
Forum: Bioinformatics 11-09-2010, 12:20 AM
Replies: 38
Views: 9,370
Posted By urchgene
@adarob ...........The output from tophat...

@adarob ...........The output from tophat ..........


@HD VN:1.0 SO:sorted
@SQ SN:AM168526 LN:577
@SQ SN:AM168527 LN:592
@SQ SN:AM168543 LN:489
@SQ ...
Forum: Bioinformatics 11-06-2010, 11:57 AM
Replies: 38
Views: 9,370
Posted By urchgene
@adarob ............when i use output from tophat...

@adarob ............when i use output from tophat

the error report is:

[bam_header_read] EOF marker is absent.
File stub_header.sam doesn't appear to be a valid BAM file, trying SAM...
Error:...
Forum: Bioinformatics 11-05-2010, 11:54 AM
Replies: 38
Views: 9,370
Posted By urchgene
@adarob.........thanks a million for the quick...

@adarob.........thanks a million for the quick reply

i used the bam as you said..........and sorted with cufflinks recommendation

sort -k 3,3 -k 4,4n tophat_out > tophat_out.sam.sorted

then...
Forum: Bioinformatics 11-05-2010, 05:25 AM
Replies: 38
Views: 9,370
Posted By urchgene
converting from sam to bam

someone please help, i am really stuck here.................

i am using this command to convert result from the newest version of Tophat from sam to bam....

samtools view -bS tophat_out.sam >...
Forum: Bioinformatics 11-05-2010, 12:02 AM
Replies: 38
Views: 9,370
Posted By urchgene
@adarob..............i used bowtie for the...

@adarob..............i used bowtie for the alignment and my headers are same as those posted by caddymob.

@adarob, i will also like to get your email if possible. email me with yahoo on same...
Forum: Bioinformatics 11-04-2010, 06:00 AM
Replies: 38
Views: 9,370
Posted By urchgene
tophat solid output to cufflinks...

Hi,

I am trying to use the new cufflinks to get differential expression from tophat ouput of solid but i get this kind of error:

Error: sort order of reads in BAMs must be the same

but the...
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