User: dfernan

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dfernan600
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600
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3 years, 4 months ago
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Posts by dfernan

<prev • 82 results • page 1 of 9 • next >
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Answer: A: The Easiest/Fastest Way To Get From Bam To Tpm Or Rpkm
... Easiest means wrong in this case, since one cannot possibly get a right estimate for RPKMs in an RNA-Seq experiment without proper handle of multiple alignments. I'd say the easiest and still right way to do it is to use Express/Cufflinks/RSEM/etc. - they produce RPKM estimates, and RSEM produces R ...
written 3.5 years ago by dfernan600
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Comment: C: Rna-Seq Paired End 76 Bp Read Data From Sra To Fastq To Bam
... @ashutoshmits, thanks this is v helpful. I will need to figure out some of the details about their fq files but this is a good start. ...
written 3.7 years ago by dfernan600
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Comment: C: Rna-Seq Paired End 76 Bp Read Data From Sra To Fastq To Bam
... @ashutoshmits thanks. Though to be honest more than ready-to-run pipelines I am interested in knowing the steps to go from SRA rna-seq file dumps to alignments... I could build my own wrapper if I know the steps but so far they seem to be far from standard and was wondering if someone has good expe ...
written 3.7 years ago by dfernan600
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Rna-Seq Paired End 76 Bp Read Data From Sra To Fastq To Bam
... Hi, I was wondering if anyone has written a wrapper to process SRA files from SRA to fastq, then do some QC on the fastq and finally map them to the hg19 genome with aligner of preference. If not, I would be more interested to hear on which steps are definitely necessary. My Data: rna-seq FULL R ...
sra fastq bam written 3.7 years ago by dfernan600 • updated 3.7 years ago by Ashutosh Pandey11k
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Comment: C: Splice-Aware Aligners Versus Genomic Aligners To Transcriptome
... @sean thanks, good point but I plan to uSe the alignments for transcript/gene expression estimation with one of the many available software such as bitseq, express, rsem, etc. My concern is forcing the alignments into "known" annotations and what is the effect of that. ...
written 3.8 years ago by dfernan600
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Comment: C: Splice-Aware Aligners Versus Genomic Aligners To Transcriptome
... @ashutosmits well, if it's not in the transcriptome GTF you are absolutely right but in principle the GTF contain all the alternative variants... ...
written 3.8 years ago by dfernan600
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Comment: C: Splice-Aware Aligners Versus Genomic Aligners To Transcriptome
... @Chris, I am using mouse transcriptome (ensembl, refseq, gencode, any transcriptome one can think of), with respect to its reliability I have the feeling is still a matter under debate... I do not care about novel splice variants but I am trying to asses the pitfalls or (none) pitfalls of approach ( ...
written 3.8 years ago by dfernan600
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Splice-Aware Aligners Versus Genomic Aligners To Transcriptome
... Hi, I have a question regarding the alignment of RNA-Seq data. Let us consider the following two strategies: (1) Genome ALigner to Transcriptome. E.g., use bowtie to align the reads to a fasta file with all transcript sequences - strategy used by several DE software, bitseq, RSem, mmseq, etc. ( ...
alignment written 3.8 years ago by dfernan600 • updated 3.4 years ago by Charles Warden4.9k
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Comment: C: Genomic Bam To Transcriptome Bam
... Hi Sean, thanks. The problem is that if I map directly to the transcripts I loose the ability to build new transcripts, find splice junctions, etc. Also in many cases I am dealing with totalRNA experiments so mapping only to transcripts I loose many reads. Let us say I already mapped all my data ...
written 3.8 years ago by dfernan600
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Genomic Bam To Transcriptome Bam
... Hi, I was looking for a tool to convert a bam file in genomic coordinates to transcriptomic coordinates (using a GTF reference). Is there a fast way to do this for large bam files? Such tool would filter out reads that do not map to any transcript. Let me know if you have any suggestions, Thank ...
bam samtools written 3.8 years ago by dfernan600 • updated 22 months ago by ngsbioinformatics30

Latest awards to dfernan

Appreciated 3.5 years ago, created a post with more than 5 votes. For Where Were The Human Genome Reference Samples Taken From?
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: Download Geo Tar File Automatically From Linux/Unix
Good Question 3.5 years ago, asked a question that was upvoted at least 5 times. For Where Were The Human Genome Reference Samples Taken From?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Trim/Remove Reads With Adapters From Illumina Rna-Seq Experiment
Popular Question 3.5 years ago, created a question with more than 1,000 views. For List Of All Transcription Factors In Human
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Download Geo Tar File Automatically From Linux/Unix
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Extract Only Uniquely Mappable Reads From Bam Files
Voter 3.5 years ago, voted more than 100 times.
Supporter 3.5 years ago, voted at least 25 times.
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Download Geo Tar File Automatically From Linux/Unix
Student 3.5 years ago, asked a question with at least 3 up-votes. For Where Were The Human Genome Reference Samples Taken From?
Student 3.5 years ago, asked a question with at least 3 up-votes. For List Of All Transcription Factors In Human

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