User: Payal

gravatar for Payal
Payal30
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30
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4 hours ago
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1 year, 5 months ago
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Posts by Payal

<prev • 15 results • page 1 of 2 • next >
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Can we concatenate two fastq files from same sample but different runs
... Hi, I have two paired end file sets for a sample. Forward: sample_R1_001.fastq.gz, sample_R1_002.fastq.gz Reverse sample_R2_001.fastq.gz, sample_R2_002.fastq.gz This is not a multilane case. They were two separate runs from the same sample aliquot!! 1. Should I concat R1_001 and R1_002 fast ...
rna-seq sequencing written 2 days ago by Payal30
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Htseq Count Error
... I was running Htseq count. htseq-count --format bam --additional-attr=gene_name --idattr=gene_id --order pos -t exon TS11_S28_merged_PE.bam example.gtf > count.txt I encountered this following error: Error occured when processing SAM input (record #443898 in file TS11_S28_merged_PE.bam ...
rna-seq written 19 days ago by Payal30 • updated 18 days ago by Devon Ryan80k
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How to create EGFP GTF file?
... Hi, I am analyzing RNA Seq data with EGFP. I need to get the count of EGFPs for samples. So I am thinking to align the fastq files to the EGFP sequence concatenated to the reference genome and then get the counts using HTseq counts. I have the EGFP.fa file, but how to create the EGFP GTF file as th ...
rna-seq written 7 weeks ago by Payal30 • updated 7 weeks ago by genomax49k
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Comment: C: 3 prime tag counting RNA Seq
... Yes its consistent among all samples..I aligned the fastq files to reference genome via Hisat2. I used Picard RNASeq Metrics to plot this graph. I just got to know this is FAC sorted data and it seems FAC sorted samples show this kind of 3prime bias..so i think i have to figure out how to do 3 prim ...
written 11 weeks ago by Payal30
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Comment: C: 3 prime tag counting RNA Seq
... This is how the graph looks,https://ibb.co/c7ou2H.. Is this normal? ...
written 11 weeks ago by Payal30
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3 prime tag counting RNA Seq
... Hi, I am currently working on an RNA Seq dataset, which has some 3 ' bias (I found that out by Picard RNASeq Metrics). So I was suggested to perfotm 3 prime tag counting. I came across this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3954844/ Can someone please explain to me how they are ...
rna-seq written 11 weeks ago by Payal30 • updated 5 weeks ago by Biostar ♦♦ 20
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Answer: A: RNA SEQ ERCC
... What I did to make it work: Previously I installed Tophat 2.1.1 and Bowtie 2.2.5 via Bioconda. I was getting the error because for some reason these versions of Tophat and Bowtie doesn't work together. So I installed Tophat from Source on my system. First I installed 2.1.1 - the plain topahat ru ...
written 5 months ago by Payal30
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Comment: C: RNA SEQ ERCC
... Yup I did look into this post while looking for answers... another problem I found was if the genome and gtf files don’t have same annotation then it can throw errors, so I downloaded both the gtf and genome fa file from Ensemble db!!! ...
written 6 months ago by Payal30
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Comment: C: RNA SEQ ERCC
... Thanks... let me try those two options !!! ...
written 6 months ago by Payal30
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Comment: C: RNA SEQ ERCC
... For now thats the only server I have..we are trying to increase our capabilities!! But for now thats all I have got to work with!! I am sorry but I don't have an answer to why they included ERCC spikeins because neither was I not involved in the study design or the wet lab part of the experiment. A ...
written 6 months ago by Payal30

Latest awards to Payal

Supporter 4 months ago, voted at least 25 times.
Popular Question 10 months ago, created a question with more than 1,000 views. For HISAT2 or Tophat2
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to download raw sequence data from GEO/SRA

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