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Forum: Bioinformatics 10-25-2016, 05:26 PM
Replies: 10
Views: 4,381
Posted By zhanghao
another question is: I have 3 pairs of...

another question is:

I have 3 pairs of pair-end fastq data sets, how to set them as input? In hisat2, I can use "-1 read_A_1.fq,reads_B_1.fq,reads_C_1.fq -2 read_A_2.fq,reads_B_2.fq,reads_C_2.fq",...
Forum: Bioinformatics 10-25-2016, 05:19 PM
Replies: 10
Views: 4,381
Posted By zhanghao
BBmap can not produce sorted bam

I used BBmap to map RNAseq data with the command:
/home/bac/software/bbmap/bbmap.sh in1=CYP51C_2_1.fq.gz in2=CYP51C_2_2.fq.gz ref=genome.fasta nodisk out=cyp51c_bb.sam bamscript=bs.sh; sh bs.sh
...
Forum: Bioinformatics 08-19-2016, 05:35 AM
Replies: 33
Views: 4,423
Posted By zhanghao
help

Dear yzzhang

Have you resovled this problem? I came accross the same problem!
Forum: Bioinformatics 08-19-2016, 04:02 AM
Replies: 2
Views: 1,807
Posted By zhanghao
Smile RepeatScout and RepeatModeler error

I want to use RepeatScout working for RepeatModeler to search for repeats. When I installed RepeatScout, I used "make" command according to README. But it is showed many warning beleow:
...
Forum: Bioinformatics 02-08-2016, 11:13 AM
Replies: 0
Views: 762
Posted By zhanghao
Trinity install error

My systerm is ununtu. When I install Trinity wieh make, the error is :

config.status: executing libtool commands
make[1]: entering dictionary...
Forum: Bioinformatics 01-04-2016, 07:16 AM
Replies: 0
Views: 823
Posted By zhanghao
How to assemible pacbio and 454 contif?

I have sequenced a bacteral using 454 and now get many 454 contig (format is xxxx.phd.1). Now I use pacbio to sequence it again. I want to assemble them together. I do not have the 454 raw data and...
Forum: Bioinformatics 11-08-2015, 04:13 PM
Replies: 16
Views: 5,124
Posted By zhanghao
Yes, I used the real path...

Yes, I used the real path /home/lydia/bbmap/bbmap.sh. And when I run bbmap, I just cd to the bbmap folder and type bbmap.sh.
Forum: Bioinformatics 11-08-2015, 06:47 AM
Replies: 16
Views: 5,124
Posted By zhanghao
my operating system is ubuntu 14.04

my operating system is ubuntu 14.04
Forum: Bioinformatics 11-08-2015, 06:41 AM
Replies: 16
Views: 5,124
Posted By zhanghao
chmod can not resolve this problem. It is useless!

chmod can not resolve this problem. It is useless!
Forum: Bioinformatics 11-08-2015, 06:30 AM
Replies: 16
Views: 5,124
Posted By zhanghao
I install bbmap according to the readme file. But...

I install bbmap according to the readme file. But when I run bbmap.sh, it showed "commond not found". I do not know why? I checked the java using java -version, java8 has been installed. Could you...
Forum: Bioinformatics 11-08-2015, 03:48 AM
Replies: 16
Views: 5,124
Posted By zhanghao
I found bbmap plugin in generous, so I can do it...

I found bbmap plugin in generous, so I can do it with geneious and compared them.
Forum: Bioinformatics 11-07-2015, 06:25 PM
Replies: 16
Views: 5,124
Posted By zhanghao
picture in this floor

picture in this floor
Forum: Bioinformatics 11-07-2015, 06:05 PM
Replies: 16
Views: 5,124
Posted By zhanghao
the picture

the picture
Forum: Bioinformatics 11-07-2015, 05:59 PM
Replies: 16
Views: 5,124
Posted By zhanghao
Compare hisat2 and tophat

I tried to used hisat2 to instead of tophat2 and compared the results. As shown in the picture (attachment) in IGV, there are many grey lines in the hisat2 result (upper one), means many reads were...
Forum: Bioinformatics 11-07-2015, 12:05 AM
Replies: 3
Views: 4,955
Posted By zhanghao
You are right, it seems the mus.gtf lack...

You are right, it seems the mus.gtf lack something. I just download this gtf file from ensembl at random. I try other gtf files, they are all ok!

But I found an another problem. When I run...
Forum: Bioinformatics 11-05-2015, 10:59 PM
Replies: 3
Views: 4,955
Posted By zhanghao
question about hisat2

I want to use hisat2. According to the manual, "Use extract_splice_sites.py (in the HISAT2 package) to extract splice sites from a GTF file", I do it as:
bac@bac-X10DAi:~/hisat2-2.0.0-beta$ python...
Forum: Bioinformatics 11-03-2015, 06:54 AM
Replies: 0
Views: 1,029
Posted By zhanghao
Tophat plugin in geneious

I used tophat plugin in geneious to map my RNAseq data, but I found the result is much worse than using command line (tophat), many introns are not well mapped. You can see the picture of my setting...
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