Forum: Bioinformatics
06-30-2016, 03:10 AM
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Replies: 3
Views: 4,571
Hi, the problem is caused by the redundancy of...
Hi, the problem is caused by the redundancy of the QTL file. There are many line with the same start and end position, if you using the abbreviation as ID, there will be all the same, just like the...
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Forum: Bioinformatics
12-03-2015, 07:33 PM
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Replies: 2
Views: 2,174
Hi JonB,
Have you resolved this problem? I...
Hi JonB,
Have you resolved this problem? I have encountered the same problem. But I can run the gamp without error on one compute node, but with problem on another compute node. Is this caused by...
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Forum: Bioinformatics
09-04-2015, 07:32 AM
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Replies: 5
Views: 4,035
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Forum: Bioinformatics
06-02-2015, 05:04 PM
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Replies: 18
Views: 14,202
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Forum: Bioinformatics
05-03-2015, 03:33 AM
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Replies: 8
Views: 8,169
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Forum: Bioinformatics
04-28-2015, 02:50 AM
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Replies: 3
Views: 3,611
What use of MEDIAN_CV_COVERAGE
According to the definition, MEDIAN_CV_COVERAGE is "The median CV of coverage of the 1000 most highly expressed transcripts. Ideal value = 0." I think the variation should be very large, because...
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Forum: Bioinformatics
04-27-2015, 04:59 AM
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Replies: 4
Views: 4,206
The problem still exist for cufflinks version...
The problem still exist for cufflinks version 2.2.1. I checked One example that one gene without any reads hit, be reported FPKM 0. However, not all genes without any reads hit were reported. How to...
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Forum: RNA Sequencing
04-26-2015, 02:03 AM
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Replies: 1
Views: 1,738
please take a look at filtercuffcompare from ...
please take a look at filtercuffcompare from seqscripts: https://github.com/roryk/seqscripts#filtercuffcompare
I have searched around found nobody has used this script here. I have tested this...
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Forum: Bioinformatics
04-21-2015, 04:37 PM
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Replies: 6
Views: 8,485
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Forum: Bioinformatics
04-16-2015, 07:35 PM
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Replies: 132
Views: 54,914
Hi Martin,
Thanks for your reply.
For...
Hi Martin,
Thanks for your reply.
For the first question, I have initialize a issue at github: https://github.com/marcelm/cutadapt/issues/120
For the second question, It just like the first...
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Forum: Bioinformatics
04-16-2015, 07:29 AM
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Replies: 132
Views: 54,914
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Forum: Bioinformatics
04-16-2015, 07:23 AM
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Replies: 132
Views: 54,914
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Forum: Bioinformatics
04-14-2015, 06:16 PM
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Replies: 132
Views: 54,914
Hi Martin,
Great software!
I want to...
Hi Martin,
Great software!
I want to use cutadapt for PacBio CCS data. However, the CCS data have the adaptor/primer in the middle of the long sequence, just like the following example:
...
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Forum: Bioinformatics
11-15-2014, 12:35 AM
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Replies: 5
Views: 4,035
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Forum: Bioinformatics
08-14-2014, 07:13 PM
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Replies: 2
Views: 4,272
The same question, more detail:
I have the...
The same question, more detail:
I have the gene ontology annotation file in obo format and gene association file in gaf2 format. I want to visualize them with the purpose:
1. how many and what...
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Forum: Bioinformatics
07-12-2014, 04:14 PM
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Replies: 1
Views: 2,951
Hi uqfgaiti,
have a look at this link: ...
Hi uqfgaiti,
have a look at this link:
http://www.broadinstitute.org/gsea/doc/GSEAUserGuideTEXT.htm#_Preparing_Data_Files
For customized species, you can create your own gene set files for...
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Forum: Bioinformatics
07-12-2014, 07:55 AM
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Replies: 8
Views: 3,184
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Forum: Bioinformatics
07-12-2014, 07:13 AM
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Replies: 8
Views: 3,184
Hi kmcarr, thank you for the reply.
...
Hi kmcarr, thank you for the reply.
Actually, I have done my work in the steps:
1. mapped fastq of the reads with quality solexa 1.3, like:
@FCC22UBACXX:2:2112:11384:88500#ACACGCGG/1...
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Forum: Bioinformatics
07-11-2014, 07:16 AM
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Replies: 8
Views: 3,184
Thank kmcarr and blancha's reply.
More...
Thank kmcarr and blancha's reply.
More question:
When I use the fastq with the base quality like this:
@FCC22UBACXX:2:1101:1463:2233#ACACGCGG
TGGTCTTCTAAATATTGTCTGAGGGCTCCGTAAGCCTGTGTTTTAGCAC...
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Forum: Bioinformatics
07-11-2014, 12:10 AM
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Replies: 8
Views: 3,184
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Forum: RNA Sequencing
10-20-2013, 08:02 PM
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Replies: 6
Views: 2,576
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Forum: Bioinformatics
09-05-2013, 06:27 PM
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Replies: 9
Views: 16,619
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Forum: Bioinformatics
09-05-2013, 06:18 PM
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Replies: 9
Views: 16,619
Hi,
still question here:
for this pair...
Hi,
still question here:
for this pair reads, i have sort the bam by the query name, they were uniquely and properply mapped. However, with 0 mapQ. According to the above mentioned method, they...
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Forum: Bioinformatics
08-19-2013, 01:25 AM
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Replies: 1
Views: 1,726
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Forum: Bioinformatics
08-18-2013, 08:24 PM
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Replies: 5
Views: 5,781
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