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User: nalandaatmi

gravatar for nalandaatmi
nalandaatmi • 90
Reputation:
90
Status:
New User
Location:
United States
Last seen:
5 years ago
Joined:
5 years, 4 months ago
Email:
n**********@gmail.com

Posts by nalandaatmi

<prev • 52 results • page 1 of 6 • next >
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Comment: C: Cuffdiff terminated after GffObj::getSpliced() error
... 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 5.1 years ago by nalandaatmi • 90 • updated 13 months ago by _r_am ♦ 32k
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Comment: C: Cuffdiff terminated after GffObj::getSpliced() error
... 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 5.1 years ago by nalandaatmi • 90 • updated 13 months ago by _r_am ♦ 32k
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Comment: C: Cuffdiff Error With Mouse Mm9 Genome Reference
... 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 5.1 years ago by nalandaatmi • 90 • updated 13 months ago by _r_am ♦ 32k
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Comment: C: Output files are empty after adapter trimming using trim galore
... 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 ...
written 5.2 years ago by nalandaatmi • 90 • updated 13 months ago by _r_am ♦ 32k
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Comment: C: Output files are empty after adapter trimming using trim galore
... Hi, Yeah, the reads are contaminated with adapter sequence. ...
written 5.2 years ago by nalandaatmi • 90
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Output files are empty after adapter trimming using trim galore
... 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 $HOME/.local/bin/cutadapt Output files: 2004_GCGTATCA_L002_R1.all_val_1.fq  and 20 ...
rnaseq trimming adapter trimgalore written 5.2 years ago by nalandaatmi • 90 • updated 5.2 years ago by h.mon ♦ 32k
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Comment: C: output SAM file from STAR aligner looks incomplete
... Dear Michael, Yes my trimmed fastq files are empty. Do I need to start new question? I used trim galore for adapter trimming. This is the summary of trim galore === Summary === Input filename: //Sample_2002/2002_AGCTAGTG_L002_R1.all.fastq.gz Total reads processed: ...
written 5.2 years ago by nalandaatmi • 90 • updated 13 months ago by _r_am ♦ 32k
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Comment: C: output SAM file from STAR aligner looks incomplete
... Dear Michael, Why did you not use a genome annotation file during the genome generation step to make full use of spliced alignments?Do you mean human GTF file? No I didn't use it. Thanks for making a note of it. I will try to create new index file based on GTF file. Please find the content of `Sam ...
written 5.2 years ago by nalandaatmi • 90 • updated 13 months ago by _r_am ♦ 32k
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output SAM file from STAR aligner looks incomplete
... Dear All, I am using STAR alignment for aligning my fastq reads from human DNA against human reference genome. Steps followed in installing STAR alignment: 1) Using git clone https://github.com/alexdobin/STAR.git. I cloned STAR directory in my linux machine.  [software@gw2 STAR]$ ls bin  CHANGES ...
aligner alignment star dnaseq written 5.2 years ago by nalandaatmi • 90
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Comment: C: Strand specific protocol for bowtie2 alignment
... 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 ...
written 5.2 years ago by nalandaatmi • 90 • updated 14 months ago by _r_am ♦ 32k

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Rising Star 5.1 years ago, created 50 posts within first three months of joining.
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