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Search: Posts Made By: zillur
Forum: Bioinformatics 05-24-2017, 09:52 AM
Replies: 4
Views: 12,428
Posted By zillur
Having the same problem, trying to resolve in different ways but noting working

Hi there,
I was trying to install this tool in my centos7 workstation but having problem. I tried to google and also tried all the possible solution but nothing works. I tried the code by "brentp"...
Forum: Bioinformatics 03-04-2017, 07:28 AM
Replies: 0
Views: 1,366
Posted By zillur
ID conversion in a csv from a text file entry

Hi there,
I have a csv file contains gene symbol for different orthogroups. I found KEGG title for each gene. Now I want to replace the gene symbol in the csv file with the KEGG title. Is it...
Forum: Bioinformatics 11-23-2016, 11:59 AM
Replies: 0
Views: 1,700
Posted By zillur
Problem with orthofinder and dlacpar

Hi there,
Hope this mail will find you in sound. I was trying to install dlcpar in my linux workstation. I failed everytime. I was trying in many ways but still no luck. Here are the error messages:...
Forum: Bioinformatics 10-14-2016, 12:37 PM
Replies: 13
Views: 3,107
Posted By zillur
Thank you very much. Got it. Best Regards ...

Thank you very much. Got it.

Best Regards
Zillur
Forum: Bioinformatics 10-10-2016, 11:30 AM
Replies: 13
Views: 3,107
Posted By zillur
Thank you very much for your valuable...

Thank you very much for your valuable suggestions. The code perfectly converted the matrix into a binary matrix. But the problem is I can't load the new csv file in R as it is:
[zillur@genomics...
Forum: Bioinformatics 10-07-2016, 12:56 PM
Replies: 10
Views: 4,195
Posted By zillur
Thank your very much. I have tried this: But it...

Thank your very much. I have tried this: But it doesn't resolve all:
(qiime191) [zillur@genomics final]$ head new_sorted_1.fasta
>M00365:7:000000000-A48JK:1:1101:10000:14343...
Forum: Bioinformatics 10-07-2016, 09:43 AM
Replies: 13
Views: 3,107
Posted By zillur
Thank you very much for your script. I was trying...

Thank you very much for your script. I was trying to run, but:
[zillur@genomics Results_Sep26]$ python matrix_convert_binary.py Orthogroups.csv
Traceback (most recent call last):
File...
Forum: Bioinformatics 10-06-2016, 02:39 PM
Replies: 9
Views: 15,753
Posted By zillur
Hi there, I was trying to sort my fasta file...

Hi there,
I was trying to sort my fasta file according to the script from this thread:awk 'BEGIN{RS=">"} NR>1 {gsub("\n", "\t"); print ">"$0}' new_15.fasta | sort -t $'\t' -k1d,1| awk '{sub("\t",...
Forum: Bioinformatics 10-06-2016, 01:00 PM
Replies: 10
Views: 4,195
Posted By zillur
Thanks. Yeah sure. I wanted to create fastq...

Thanks.
Yeah sure. I wanted to create fastq file using my .qual ahd fasta file using qiime. But it gaves me:
KeyError: 'QUAL header (M00365:7:000000000-A48JK:1:1101:14885:1320) does not match...
Forum: Bioinformatics 10-06-2016, 12:39 PM
Replies: 10
Views: 4,195
Posted By zillur
Thank you very much. alphabetically/numerically...

Thank you very much. alphabetically/numerically whichever convenient.

Best Regards
Zillur
Forum: Bioinformatics 10-06-2016, 11:06 AM
Replies: 10
Views: 4,195
Posted By zillur
Sorting fasta file according to header

Hi there,
I have a fasta file like this:
[zillur@genomics filter]$ head new_12.fasta
>000000M00365:7:000000000-A48JK:1:1110:10044:9619...
Forum: Bioinformatics 10-06-2016, 11:00 AM
Replies: 1
Views: 2,245
Posted By zillur
Anybody has any suggestion about this matter? ...

Anybody has any suggestion about this matter?

I appreciate your comments.

Best regards
Zillur
Forum: Bioinformatics 10-06-2016, 10:54 AM
Replies: 13
Views: 3,107
Posted By zillur
Thank you very much for your reply. Exactly I...

Thank you very much for your reply. Exactly I want to do this. But how can replace this?

Thanks for your suggestions.
Best Regards
Zillur
Forum: Bioinformatics 10-05-2016, 06:24 PM
Replies: 0
Views: 1,241
Posted By zillur
Getting error in creating heatmap from Orthogroups.csv

Hi there,
After running orthfinder, I got orthgroups.csv. I wanted to create a heat map using the attached script. But it gives me:

Error in matrix(0, nrow = nrow(m), ncol = max(m, na.rm = TRUE))...
Forum: Bioinformatics 10-05-2016, 01:39 PM
Replies: 3
Views: 1,353
Posted By zillur
Thanks again. How can sort the file according to...

Thanks again. How can sort the file according to header?

Best Regards
Zillur
Forum: Bioinformatics 10-05-2016, 01:28 PM
Replies: 3
Views: 1,353
Posted By zillur
Thank you very much. That exactly what I wanted. ...

Thank you very much. That exactly what I wanted.
>M00365:7:000000000-A48JK:1:1101:14885:1320
AAAAAAFF@BBBBGGGGCEAFEFEEEEGDFGGHGGE?AAFHFEECEGGCEEFFFHEEGE?...
Forum: Bioinformatics 10-05-2016, 09:39 AM
Replies: 1
Views: 2,245
Posted By zillur
samtools mpileup, neither ploidy nor ploidy file given

Hi there,
I was trying to psmc analysis of apicomplexan genome using the attached script. It does running perfectly for many mammalian genomes (human, cat, dog, etc.). For this organisms I am...
Forum: Bioinformatics 10-05-2016, 09:27 AM
Replies: 3
Views: 1,353
Posted By zillur
Convert intiger into ascii character in a .qual file

Hi there,
I have a quality file like this:

>M00365:7:000000000-A48JK:1:1101:14885:1320
32 32 32 32 32 37 37 31 33 33 33 33 38 38 38 38 34 36 32 37 36 37 36 36 36 36 38 35 37 38 38 39 38 38 36 30...
Forum: Bioinformatics 10-05-2016, 09:21 AM
Replies: 13
Views: 3,107
Posted By zillur
Thank you very much for your comment. I want a...

Thank you very much for your comment. I want a matrix like:

genome1 genome2 genome3
gene1 1 0 0
gene2 0 0 0
gene3 1 1 1
gene4 0 ...
Forum: Bioinformatics 10-04-2016, 10:52 AM
Replies: 2
Views: 1,921
Posted By zillur
Thank you very much. After adding this argument,...

Thank you very much. After adding this argument, it works perfectly now. Thanks again.

Best Regards
Zillur
Forum: Bioinformatics 10-04-2016, 10:43 AM
Replies: 13
Views: 3,107
Posted By zillur
Thank you very much for your suggestions. Yeah. I...

Thank you very much for your suggestions. Yeah. I have tried orthofinder and it gave me outputs. I wanted to run orthomcl to compare, maybe its not necessary now. Do you have any suggestions how can...
Forum: Bioinformatics 10-03-2016, 03:46 PM
Replies: 2
Views: 1,921
Posted By zillur
Abyss Installation problem

Hi there,
I was trying to installation in my linux workstation. I have downloaded the package from github and tried to follow these steps:
Compiling ABySS from GitHub
===========================
...
Forum: Bioinformatics 10-03-2016, 01:36 PM
Replies: 13
Views: 3,107
Posted By zillur
Is there anybody has any idea? Please. I...

Is there anybody has any idea? Please. I appreciate your helps.

Best Regards
Zillur
Forum: Bioinformatics 09-27-2016, 08:07 AM
Replies: 13
Views: 3,107
Posted By zillur
Orthomcl running problem

Hi there,
I was trying to run orthomcl in my linux workstation. I am facing this problem:
[root@genomics bin]# ./orthomcl-pipeline -i /home/zillur/Desktop/zillur/phd/orthomcl -o...
Forum: Bioinformatics 01-25-2016, 11:52 AM
Replies: 0
Views: 1,767
Posted By zillur
PSMC, having to generate diploid.psmc file

Hi there,
I have downloaded fasta assembly from hamster:...
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