User: Payal

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Payal30
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2 years, 2 months ago
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Posts by Payal

<prev • 20 results • page 1 of 2 • next >
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Answer: A: error opening file after QIIME script: add_qiime_labels.py
... I had the same problem. Two things figured: 1. The file should be fasta files. So convert your fastq files to fastq file using qiime scipts - **convert_fastqual_fastq.py** That will create .fna files 2. Now while you are running the **add_qiime_labels.py**, the mapping file name should be exactly ...
written 3 days ago by Payal30
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Nextseq and Miseq data output difference?
... Hi, Is it ok to run a Mixcr pipeline on a TCR sequencing dataset, half of which was processed on Nextseq and half on Miseq? What is the major difference among Nextseq and Miseq platforms? Thanks, Payal ...
sequencing written 25 days ago by Payal30 • updated 25 days ago by Charles Warden6.4k
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qiime 1 biom format error
... Hi, I installed qiime 1 via bioconda and am trying to run the script differential_abundance.py. This has dependencies with some R packages like biom format, which is giving me the following error: I ran: differential_abundance.py -i otu_table_L2.biom -a DESeq2_nbinom -m mappingfile.txt -c Disease - ...
software error R sequencing written 3 months ago by Payal30
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Comment: C: Qiime - problem with biom package in normalization
... How to do that ? I typed: > install.packages(biom_0.3.8.tar.gz) Error in install.packages(biom_0.3.8.tar.gz) : object 'biom_0.3.8.tar.gz' not found ...
written 3 months ago by Payal30
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Comment: C: Htseq Count Error
... Hi, I actually was able to get around this by filtering the BAM files for mapped and paired-end reads using samtools. Eg: samtools view -b -F 4 bam_file > mapped_bam_file samtools view -bf 1 bam_file > pairedend_bam_file After filtering the BAM files, HTSeq eventually worked for my dataset ...
written 5 months ago by Payal30
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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 9 months ago by Payal30 • updated 7 months ago by Biostar ♦♦ 20
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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 9 months ago by Payal30 • updated 9 months ago by Devon Ryan88k
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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 10 months ago by Payal30 • updated 10 months ago by genomax63k
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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 months 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 months ago by Payal30

Latest awards to Payal

Popular Question 14 days ago, created a question with more than 1,000 views. For HISAT2 or Tophat2
Great Question 8 weeks ago, created a question with more than 5,000 views. For HISAT2 or Tophat2
Supporter 13 months ago, voted at least 25 times.
Popular Question 19 months ago, created a question with more than 1,000 views. For HISAT2 or Tophat2
Teacher 19 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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