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Forum: Bioinformatics 09-22-2016, 05:52 AM
Replies: 5
Views: 3,056
Posted By newfie
Actually there are two output files output.sam...

Actually there are two output files output.sam and output_E1.sam in the home directory. both of them gives the same output as i had mentioned earlier. Out of curiosity, i tired with fastq files...
Forum: Bioinformatics 09-22-2016, 01:08 AM
Replies: 5
Views: 3,056
Posted By newfie
I tried it again with samtools view -bSh...

I tried it again with samtools view -bSh output_E1.sam > output_E1.bam , but the problem is not solved, it just keeps on giving the same output
Forum: Bioinformatics 09-21-2016, 09:15 AM
Replies: 5
Views: 3,056
Posted By newfie
Probelem with SAM file created by Bowtie2

Hello everyone,

I created a bowtie index from a fasta file which was merged from 4 individual fasta file. One is from miRBase, two from RFAM coressponding to tRNA and other non coding RNA and the...
Forum: Bioinformatics 07-12-2016, 04:31 AM
Replies: 0
Views: 1,143
Posted By newfie
Problem with mirdeep2

I have a problem with mapper.pl when i input my fasta file containing the reads.

here is the command and the error that i get:

mapper.pl N1_S1.fa -c -p ~/Desktop/bowtiebuild/cod_index -m -s...
Forum: Bioinformatics 04-07-2016, 08:27 AM
Replies: 1
Views: 1,233
Posted By newfie
Problem creating index files from reference genome using miRDeep*

Hi guys,

I am using miRDeep and i wanted to create index files to be used in miRDeep*. But i am getting an error every time i execute the command

This is their instructions on the mannual how...
Forum: Bioinformatics 03-11-2016, 01:07 AM
Replies: 6
Views: 1,849
Posted By newfie
^^^^ or in other words i am wondering if there is...

^^^^ or in other words i am wondering if there is a TRAILCROP option in Trimmomatic ;)
Forum: Bioinformatics 03-11-2016, 12:56 AM
Replies: 6
Views: 1,849
Posted By newfie
Trimmoatic: Command for cutting bases from the start and end of the read

Hi everyone,

I am working with small non coding RNA data. I removed my adapter sequences from my data. However, there are random miRS of 4 bases attached to both the start and end of the reads....
Forum: Bioinformatics 03-02-2016, 09:47 AM
Replies: 8
Views: 6,385
Posted By newfie
Hi all, This is my first post in seqanswers....

Hi all,

This is my first post in seqanswers. I am also working with small RNA and i found this thread more useful in understanding the different parameters used in Trimmomatic. I have just now...
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