User: mohammedtoufiq91

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Posts by mohammedtoufiq91

<prev • 19 results • page 2 of 2 • next >
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Sub-sampling RNA-seq data
... Hi, I would like to know if sub-sampling of a particular unaligned fastq file and aligned sam/bam file produce similar outputs? Is it better to sub-sample the fastq or aligned sam file? Which sub-sampling would be better? Thank you, Toufiq ...
fastq bam sam rna-seq downsampling written 9 days ago by mohammedtoufiq910
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Comment: C: Reduce number of reads from 100M to 50M in the sample from the existing RNA-Seq
... Thank you. What is -s100 parameter? Is it the read length? My data files are compressed in the fastq.gz format. Is this supported by seqtk? Are there any commands and arguments? ...
written 9 days ago by mohammedtoufiq910
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Comment: C: Reduce number of reads from 100M to 50M in the sample from the existing RNA-Seq
... Thank you. It was helpful. Does sub-sampling of a particular unaligned fastq file and aligned sam/bam file produce similar outputs? ...
written 9 days ago by mohammedtoufiq910
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Comment: C: Reduce number of reads from 100M to 50M in the sample from the existing RNA-Seq
... **Does that mean your total dataset had 100 M reads and there are ~5 samples with reads ranging from 19-28M?** There are 13 samples. Each sample was sequenced for 100 million read depth. However, the fastq files generated shows varying total number of reads for each sample as mentioned below for ins ...
written 11 days ago by mohammedtoufiq910
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Comment: C: Reduce number of reads from 100M to 50M in the sample from the existing RNA-Seq
... Thank you all for the suggestions and advise. Let me rephrase the question once again. We have generated a set of RNA-seq samples from blood tissue (non globin depleted). These are human paired-end samples with read length of 150bp with 100 million read depth. After the alignment against hg19 geno ...
written 11 days ago by mohammedtoufiq910
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Reduce number of reads from 100M to 50M in the sample from the existing RNA-Seq fastq files
... Hi, We have generated a set of RNA-seq samples from blood tissue. These are human paired-end samples with 100M reads and with read length of 150bp. I want to know if it's possible to reduce the number of reads from 100M to 50M in the sample(s) from the existing RNA-Seq fastq files generated the fac ...
reads fastq sequence rna-seq written 12 days ago by mohammedtoufiq910 • updated 8 days ago by chen1.8k
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Comment: A: RNA-seq alignment against globin genes (HBA1, HBA1, and HBB)
... Thank you all for the comments. It was helpful. ...
written 12 days ago by mohammedtoufiq910
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Comment: C: RNA-seq alignment against globin genes (HBA1, HBA1, and HBB)
... Thank you Kevin. This was helpful. From the provided comments, I understand that, I need to first align my non globin depleted samples against whole genome hg19 build. Post this, perform quantification and obtain the expression of these genes. Could you please provide any material or publication r ...
written 20 days ago by mohammedtoufiq910
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RNA-seq alignment against globin genes (HBA1, HBA1, and HBB)
... Hi, We have generated a set of RNA-seq samples from blood tissue which are non globin depleted. I want to perform the RNA-seq alignment against a set of highly abundant globin genes (HBA1, HBA2, and HBB) and identity the percentage of globin reads mapping to these genes and exclude it from the an ...
alignment rna-seq written 21 days ago by mohammedtoufiq910

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