User: nalandaatmi
nalandaatmi • 70
- Reputation:
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- United States
- Last seen:
- 3 years, 7 months ago
- Joined:
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Posts by nalandaatmi
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... Dear Devon,
When I used Ensembl mouse GTF file, I didn't encounter this error. But with the UCSC mouse GTF file, I faced the same kind of error for the different project dealing with the mouse.
Another colleague in my team did the RNAseq analysis using UCSC mouse GTF file. He generated some output ...
written 3.8 years ago by
nalandaatmi • 70
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... Dear Devon Thanks for getting back to me. I really appreciate it.
Sure I will check the file as you mentioned. I used following commands in my analysis
Tophat command:
$ tophat -p 12 -G mousegenes.gtf --library-type fr-unstranded -o tophat_out mousegenome R1.fastq R2.fastq
Cufflinks command:
$ ...
written 3.8 years ago by
nalandaatmi • 70
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... Dear Devon,
I need a help on this "Question: Cuffdiff terminated after GffObj::getSpliced() error" question. Will you be able to check this link https://www.biostars.org/p/167635/ ?
...
written 3.8 years ago by
nalandaatmi • 70
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... Hi, human Mitochondrial DNA has been sequenced.
This is what I noticed in trim galore log file:
No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default)
Path to Cutadapt set as: '/data2/test/.local/bin/cutadapt' (user defined)
1.9
Cutadapt seem ...
written 3.8 years ago by
nalandaatmi • 70
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... Hi,
Yeah, the reads are contaminated with adapter sequence.
...
written 3.8 years ago by
nalandaatmi • 70
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... Dear All,
I used trim galore for adapter trimming.
Command : trim_galore --paired -a GAGAGCGATCCTTGC -a2 AGATCGGAAGAGC 2002_AGCTAGTG_L002_R1.all.fastq.gz 2002_AGCTAGTG_L002_R2.all.fastq.gz -o ./ --path_to_cutadapt $HOME/.local/bin/cutadapt
Output files:
2004_GCGTATCA_L002_R1.all_val_1.fq and 20 ...
written 3.8 years ago by
nalandaatmi • 70
• updated
3.8 years ago by
h.mon ♦ 27k
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... Dear Michael,
Yes my trimmed fastq files are empty. Do I need to start new question?
I used trim galore for adapter trimming. This is the summary of trim galore
=== Summary ===
Input filename: //Sample_2002/2002_AGCTAGTG_L002_R1.all.fastq.gz
Total reads processed: 6,289,520
Reads ...
written 3.8 years ago by
nalandaatmi • 70
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... Dear Michael,
Why did you not use a genome annotation file during the genome generation step to make full use of spliced alignments?Do you mean human GTF file? No I didn't use it. Thanks for making a note of it. I will try to create new index file based on GTF file.
Please find the content of Samp ...
written 3.8 years ago by
nalandaatmi • 70
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... Dear All,
I am using STAR alignment for aligning my fastq reads from human DNA against human reference genome.
Steps followed in installing STAR alignment:
1) Using git clone https://github.com/alexdobin/STAR.git. I cloned STAR directory in my linux machine.
[software@gw2 STAR]$ ls
bin CHANGES ...
written 3.8 years ago by
nalandaatmi • 70
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... Thanks Sam for getting back to me. all the best for your thesis.
Reason for doing TopHat:
First, I carried out TopHat analysis. Then the bam file from TopHat used along with GTF file in HTseq-count, to get the number of reads aligned to each gene. But, from Htseq-count I couldn't get the number of ...
written 3.8 years ago by
nalandaatmi • 70
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