User: Shahzad

gravatar for Shahzad
Shahzad10
Reputation:
10
Status:
New User
Location:
Pakistan
Last seen:
2 months, 1 week ago
Joined:
3 years, 3 months ago
Email:
s****@live.com

Posts by Shahzad

<prev • 36 results • page 1 of 4 • next >
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Trinity Error, not recognizing read name formatting: [1]
... I am using Trintiy to make transcriptome assembly and it looks like something is wrong with my sequence format. I am using this data by downloading it from GEO database and SRA files are not available for this project. So, I cant use fastq-dump (if that is why it is behaving like this). Please let m ...
de novo trinity transcriptome rna-seq assembly written 12 weeks ago by Shahzad10
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Comment: C: Multiple Alignment: Protein Or Nucleotide Sequence?
... I know its pretty late reply but I hope it could help the new reader coming to this post. Both approaches are correct. All it depends upon what you want from the MSA results. i.e IF you want to know conserved/non-conserved AAs or nucleotides (which are ultimately making protein) you should do it as ...
written 9 months ago by Shahzad10
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Comment: C: FastQC not making html output report.
... I wrote the solution "./fastqc" worked for me. If this doesn't solve your problem just paste the error you are getting. I will try to solve it. ...
written 11 months ago by Shahzad10
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Answer: A: How to add tophat and bowtie to the path?
... I have solved this problem with a very easy solution. Problem occurs when you set $PATH to a directory it clears the previous paths from the system which are essential for to run the software sometimes. So, >echo PATH copy all the paths comes in the results the use >export PATH command and ...
written 11 months ago by Shahzad10
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Comment: C: How to identify the different varieties of same species in Plants?
... @Macspider Thank you for the reply. I am starting this project. So, I can opt any method. I have experience with Next Gen data and also have molecular biology skills. I just want to enlist all the options which can lead to success of this project. ...
written 11 months ago by Shahzad10
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How to identify the different varieties of same species in Plants?
... Dear All I want to establish a system to differentiate between the varieties of same species(specifically plants). Please let me know if anyone has done it with any protocol. Best Regards Shahzad ...
genome sequence next-gen sequencing written 11 months ago by Shahzad10 • updated 11 months ago by Macspider1.6k
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Comment: C: How To Deal With Duplicate Row Names Error In R
... what could the possible solution if I need to add the value and row name should remain the same. e.g instead >bl.a 1 >bl.a**.1** 2 >bl.a**.2** 3 f>oo 4 I need >bl.a 5 (adding the first 3 rows with same name) >foo ...
written 14 months ago by Shahzad10
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Comment: C: How to identify the miRNA counts column?
... I used "multicov" from bedtools. ...
written 14 months ago by Shahzad10
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Comment: C: SortMeRNA starts, pauses, never finishes
... please share the command you are using and also if you get and "verbose" which appear while running the tool. ...
written 14 months ago by Shahzad10
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How to identify the miRNA counts column?
... I have miRNA data of a plant. I aligned the reads using Bowtie (short read aligner) against miRbase database miRNAs. Then I used samtools -> bamtools -> bedtools to get the counts. Now I have counts imported into R but I am confused which column contains the counts. Please help to name all th ...
bedtools biostat ngs counts mirna written 14 months ago by Shahzad10

Latest awards to Shahzad

Popular Question 9 months ago, created a question with more than 1,000 views. For How to get counts of STAR output (sam/bam).
Popular Question 10 months ago, created a question with more than 1,000 views. For How to get counts of STAR output (sam/bam).
Popular Question 13 months ago, created a question with more than 1,000 views. For FastQC not making html output report.
Popular Question 17 months ago, created a question with more than 1,000 views. For miRNA target prediction tools

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