User: mohammedtoufiq91
mohammedtoufiq91 • 0
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Posts by mohammedtoufiq91
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... Hi,
I am currently working with the Fluidigm qRT-PCR data. There are 3 plates with total of 288 genes combined into one file (264 target genes + 8*3 (triplicate)= 24 Reference genes) with each plate consists of 96 genes (88 Target genes + 8 Reference genes) in one file. In summary, I have approxima ...
written 2 hours ago by
mohammedtoufiq91 • 0
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... Hi,
Is it possible to identify whether our specific adapters are 5' forward/reverse or 3' forward/reverse.
We are using Illumina Paired End data with the read length of 150*2. The protocol is TrueSeq mRNA stranded kit.
Thank you,
Toufiq ...
written 4 hours ago by
mohammedtoufiq91 • 0
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... Thank you. I ran this program, however, did not find any specific adapter.
./fastp -i -I -o R1.fastq.gz -O R2.fastq.gz --disable_adapter_trimming --detect_adapter_for_pe --html Report_sample.html
In the .html file, this only reports
Duplication rate
Insert size estimaion
Before/after filtering ...
written 2 days ago by
mohammedtoufiq91 • 0
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... Thank you. I was able to identify the adapters in R1.fq and R2.fq. Now, I would like to know if these are 5' forward/reverse or 3' forward/reverse. Is there are way to identify. ...
written 2 days ago by
mohammedtoufiq91 • 0
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... Hi,
I am working with the Illumina paired end unaligned data. I would like to initially identify the adapter sequences present in the data, and trim the reads accordingly. Is there are a way to identify the adapter sequences. Please assist me with this and let me know the tools to use.
Thank yo ...
written 5 days ago by
mohammedtoufiq91 • 0
• updated
5 days ago by
benformatics • 490
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... Hi,
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. I would like to find out the differentially expressed genes and perform fold change comparison between the different subjects. Please assist me with ...
written 8 days ago by
mohammedtoufiq91 • 0
• updated
8 days ago by
Bastien Hervé ♦ 3.3k
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Comment:
C: Sub-sampling RNA-seq data
... Thank you. This was helpful. ...
written 8 days ago by
mohammedtoufiq91 • 0
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... So, I understand that fastp could be used for the downsampling and subsampling data with compressed fastq files. ...
written 8 days ago by
mohammedtoufiq91 • 0
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... Thank you. In seqtk, 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 8 days ago by
mohammedtoufiq91 • 0
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98
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Comment:
C: Sub-sampling RNA-seq data
... Thank you. 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. After the alignment against hg19 genome, the alignment range is between 84-91% for different samples. Quantification process provided a rough e ...
written 9 days ago by
mohammedtoufiq91 • 0
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