Forum: RNA Sequencing
06-06-2014, 06:24 AM
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Replies: 1
Views: 1,857
Calling SNP in RNA seq
Hi All
I have assembled two mammalian transcriptome which doesn't have reference genome. I have assembled it using Trinity and now I have used varscan to call the SNP by mapping the reads to the...
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Forum: RNA Sequencing
04-07-2014, 10:58 AM
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Replies: 2
Views: 3,464
Adapter trimming
Hi
I have got the adapter sequences from company as for Illumina RNA seq data:...
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Forum: Illumina/Solexa
04-05-2014, 03:39 AM
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Replies: 1
Views: 1,424
Index sequences
Hi All
I recently got RNA seq data sequenced on Illumina, which is of single sample run on single lane. When I checked the RNA seq reads which are 94 bp in length, in RNA seq header I find that it...
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Forum: Illumina/Solexa
04-09-2013, 06:42 AM
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Replies: 9
Views: 4,466
Hi Hsueh-Ting Chu
I tried to run the...
Hi Hsueh-Ting Chu
I tried to run the EBARDenovo with the example files provided in the sample. It works fine, but when I try to run my sequences I am getting the error. I am copying the log file...
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Forum: 454 Pyrosequencing
02-21-2013, 06:36 AM
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Replies: 1
Views: 1,946
Newbler Scafolding
Hi All
I tried running the newbler 2.6. But when i use the flag -scaffold I don't get any of the three scaffold file. Can some body tell me is it possible to make scaffolds using the single end...
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Forum: Illumina/Solexa
01-25-2013, 08:39 AM
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Replies: 1
Views: 1,091
Tophat mapping Results
Hi All
I used tophat to map my 100 million base paired illumina reads after trimming with average length of 86 bp. In the bam output file generated by tophat I only find around 55 million read...
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Forum: RNA Sequencing
01-11-2013, 04:44 AM
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Replies: 38
Views: 18,953
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Forum: Bioinformatics
01-08-2013, 02:51 AM
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Replies: 0
Views: 1,299
Orthomcl for more then 2 species
Hi All
I have run the orthomcl for 4 species and having the orthologous pairs file and group file. I am confused that from these files how I can take out the 4 species orthologous sequences ids as...
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Forum: Bioinformatics
01-07-2013, 10:31 AM
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Replies: 9
Views: 2,839
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Forum: RNA Sequencing
01-07-2013, 08:55 AM
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Replies: 8
Views: 4,008
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Forum: RNA Sequencing
12-06-2012, 02:16 AM
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Replies: 37
Views: 19,858
setting up the -r parameter in tophat
Hi Glados
Reading the thread and your comments. I have a query about setting up the parameter in -r. I also tried to get the information of insert size from the sequencing lab and they said me it...
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Forum: Illumina/Solexa
11-18-2012, 01:02 PM
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Replies: 2
Views: 6,061
PolyA removal from RNA seq Illumina reads
Hi All,
I have paired end RNA seq Illumina reads. Do i need to remove the PolyA from the reads ( is it required) in the preprocessing step of Reads. What are the software to do it? .I am little...
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Forum: RNA Sequencing
10-27-2012, 11:00 AM
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Replies: 3
Views: 2,201
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Forum: Bioinformatics
10-09-2012, 01:47 AM
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Replies: 3
Views: 1,709
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Forum: Bioinformatics
10-09-2012, 01:38 AM
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Replies: 2
Views: 1,780
Dear Torst
Thank you for your reply.
1....
Dear Torst
Thank you for your reply.
1. I am using the samtools 0.1.18 version.
2. I tried what you suggested and I didn't get the error this time but it again stops at the same point and I...
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Forum: Illumina/Solexa
10-09-2012, 01:34 AM
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Replies: 3
Views: 1,959
Thank you for your reply.
1.Please let me know...
Thank you for your reply.
1.Please let me know why it can happen as I can generate 10 chromosomes in the consensus file and then it gives the error but i can see all the chromosomes in the bam...
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Forum: Bioinformatics
10-05-2012, 11:51 AM
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Replies: 8
Views: 5,154
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Forum: Bioinformatics
10-05-2012, 08:04 AM
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Replies: 8
Views: 6,610
I am also fed up of similar error
[afs]...
I am also fed up of similar error
[afs] 0:99774.498 1:110.438 2:115.064
[bcf_sync] incorrect number of fields (4 != 5) at 15:16294867
Have you found the reason for it . If you can share that...
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Forum: Bioinformatics
10-05-2012, 07:07 AM
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Replies: 2
Views: 1,780
Samtools consensus sequence error
Dear All
I am again posting this question to the Bioinformatics forum as I didn't get the answer from the Illumina forum.
I am trying to make consensus sequences using command
samtools...
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Forum: Illumina/Solexa
10-05-2012, 02:12 AM
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Replies: 3
Views: 1,959
Samtools consensus sequence error
Dear All
I am trying to make consensus sequences using command
samtools mpileup -uf ref.fa aln.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fq.
But i am getting this error:
[bcf_sync]...
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Forum: Bioinformatics
10-05-2012, 01:05 AM
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Replies: 8
Views: 5,154
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Forum: Bioinformatics
09-27-2012, 10:16 AM
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Replies: 6
Views: 3,894
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Forum: RNA Sequencing
09-27-2012, 10:02 AM
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Replies: 38
Views: 18,953
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Forum: Illumina/Solexa
09-06-2012, 03:41 AM
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Replies: 0
Views: 1,222
Tophat -r parameter setting
Hi All
I need to set the -r paramter in Tophat run, reading the posts on this made me confused. I have an insert size of 180 and the paired end reads of read length of size 100. So what would be...
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Forum: Bioinformatics
07-25-2012, 07:56 AM
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Replies: 9
Views: 2,105
tophat running error
hi All
I have installed the tophat with bowtie and samtools in the path but I am getting the error when I try to run the example file.
[2012-07-25 17:31:11] Beginning TopHat run (v2.0.4)...
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