User: mohammedtoufiq91

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Posts by mohammedtoufiq91

<prev • 19 results • page 1 of 2 • next >
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qRT-PCR data analysis steps and workflow
... 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 ...
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Identify adapter position
... 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 ...
adapter trimming rna-seq written 4 hours ago by mohammedtoufiq910
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Comment: C: Identify adapter sequences for trimming from Illumina paired end fastq files
... 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 mohammedtoufiq910
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Comment: C: Identify adapter sequences for trimming from Illumina paired end fastq files
... 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 mohammedtoufiq910
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Identify adapter sequences for trimming from Illumina paired end fastq files
... 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 ...
adapter trimming fastq qc rna-seq written 5 days ago by mohammedtoufiq910 • updated 5 days ago by benformatics490
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RNA-seq analysis data analysis pipeline
... 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 ...
quantification fc rna-seq alignment expression written 8 days ago by mohammedtoufiq910 • updated 8 days ago by Bastien Hervé3.3k
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Comment: C: Sub-sampling RNA-seq data
... Thank you. This was helpful. ...
written 8 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
... So, I understand that fastp could be used for the downsampling and subsampling data with compressed fastq files. ...
written 8 days ago by mohammedtoufiq910
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Comment: A: Reduce number of reads from 100M to 50M in the sample from the existing RNA-Seq
... 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 mohammedtoufiq910
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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 mohammedtoufiq910

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