DM Notes 1.21.16 - Revision history

Dymaghini at 18:40, 11 February 2016

2016-02-11T18:40:09Z

Dymaghini at 19:04, 21 January 2016

2016-01-21T19:04:35Z

Dymaghini: Created page with "FastQC Reports: how to read Illumina sequencing Per base sequence quality: x-axis is bp. Quality score from 0 to 40 (40 being perfect score, 20 and higher is considered good..."

2016-01-21T18:47:04Z

Created page with "FastQC Reports: how to read Illumina sequencing Per base sequence quality: x-axis is bp. Quality score from 0 to 40 (40 being perfect score, 20 and higher is considered good..."

New page

FastQC Reports: how to read

Illumina sequencing

Per base sequence quality: x-axis is bp. Quality score from 0 to 40 (40 being perfect score, 20 and higher is considered good). Whiskers could represent different things.

Per tile sequence quality: these were all read simultaneously. Put cDNA in a device about the size of palm. Since all were done through the same device, makes sense that everyone in the class has the same panel. Not sure whether red flag is a deal breaker.

Per sequence quality scores: most of the sequences have a high quality (peak at 39). Anything from 20 or higher is considered good, but there are a few reads that aren't very good (below 20).

Per base sequence content:

← Older revision		Revision as of 18:40, 11 February 2016
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	'''Kmer Content''': 'K' is a number. That table will probably go to zero when the barcodes are stripped off of the reads.		'''Kmer Content''': 'K' is a number. That table will probably go to zero when the barcodes are stripped off of the reads.
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		+	Back to home [[Dylan Maghini]]

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-FastQC Reports: how to read
+'''FastQC Reports: how to read'''
 Illumina sequencing
-Per base sequence quality: x-axis is bp. Quality score from 0 to 40 (40 being perfect score, 20 and higher is considered good). Whiskers could represent different things.
+'''Per base sequence quality''': x-axis is bp. Quality score from 0 to 40 (40 being perfect score, 20 and higher is considered good). Whiskers could represent different things.
-Per tile sequence quality: these were all read simultaneously. Put cDNA in a device about the size of palm. Since all were done through the same device, makes sense that everyone in the class has the same panel. Not sure whether red flag is a deal breaker.
+'''Per tile sequence quality''': these were all read simultaneously. Put cDNA in a device about the size of palm. Since all were done through the same device, makes sense that everyone in the class has the same panel. Not sure whether red flag is a deal breaker.
-Per sequence quality scores: most of the sequences have a high quality (peak at 39). Anything from 20 or higher is considered good, but there are a few reads that aren't very good (below 20).
+'''Per sequence quality scores''': most of the sequences have a high quality (peak at 39). Anything from 20 or higher is considered good, but there are a few reads that aren't very good (below 20).
-Per base sequence content:
+'''Per base sequence content''': first few bases are the barcodes. Barcodes for intestine (1) AGG, (2) CGG, (3) AAC, (4) AGC, (5) ACG, (6) AGA. Wiki page has file with reagents. These are all correct, so they allow us to make sense of the barcode reports that we have gotten. Remember, barcodes aren't part of the RNA sequence. Dr. Heyer and Dr. Campbell are attempting to trim. Only keeping nucleotides w/ score >15, and then should be able to match w/ genome to see which transcripts there are.