User: Payal

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Payal40
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2 years, 6 months ago
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Posts by Payal

<prev • 25 results • page 1 of 3 • next >
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Comment: C: HIsat2 bam and summary output - multiple output file type
... Thank you very much Carlo. I am also new to snakemake, so I test and periodically try to improve my script. Actually, I just tested my scirpt using the same logic that you have described here. It works perfectly now. I was going to post my updated script, coincidentally you have already posted it ...
written 4 days ago by Payal40
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Comment: C: HIsat2 bam and summary output - multiple output file type
... Thank you Devon and AT. I see what you are saying. I will try this. Will this output all sample summaries in one summary file like a log file or individual samples will output their individual summary report? ...
written 4 days ago by Payal40
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Comment: C: HIsat2 bam and summary output - multiple output file type
... Thank you Carlo. I tried this but it gives me NameError: The name 'sample' is unknown in this context. Please make sure that you defined that variable. Also note that braces not used for variable access have to be escaped by repeating them, i.e. {{print $1}} How should I fix this? ...
written 4 days ago by Payal40
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Comment: C: HIsat2 bam and summary output - multiple output file type
... I am sorry, didn't understand. Can you please elaborate? ...
written 5 days ago by Payal40
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HIsat2 bam and summary output - multiple output file type
... Hello, The general command for Hisat2 alignment is: hisat2 --threads 8 -t -p 8 --summary-file summary_txt -x /hisat2_index/index -1 read1.fastq.gz -2 read2.fastq.gz -S aligned.sam I use the following script to run my Hisat2 pipelines. The bam files I am getting are fine. My question is how ...
snakemake rna-seq sequencing written 5 days ago by Payal40 • updated 5 days ago by Carlo Yague4.6k
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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 4 months ago by Payal40
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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 4 months ago by Payal40 • updated 4 months ago by Charles Warden7.0k
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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 7 months ago by Payal40
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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 7 months ago by Payal40
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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 9 months ago by Payal40

Latest awards to Payal

Popular Question 6 weeks ago, created a question with more than 1,000 views. For HISAT2 or Tophat2
Popular Question 4 months ago, created a question with more than 1,000 views. For HISAT2 or Tophat2
Popular Question 4 months ago, created a question with more than 1,000 views. For HISAT2 or Tophat2
Great Question 6 months ago, created a question with more than 5,000 views. For HISAT2 or Tophat2
Supporter 17 months ago, voted at least 25 times.
Popular Question 23 months ago, created a question with more than 1,000 views. For HISAT2 or Tophat2
Teacher 23 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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