Go Back   SEQanswers > Applications Forums > RNA Sequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
Methyl-Seq: Lib prep (MspI;HpaII) for mouse samples causes issues for human samples F.L. Sample Prep / Library Generation 1 07-22-2015 06:04 PM
New isoform found in mouse, can we use RNAseq to find it in humans? sindrle RNA Sequencing 3 02-25-2014 08:17 PM
Contamination between samples run on the same lane MLog Illumina/Solexa 4 12-08-2013 05:42 PM

Thread Tools
Old 06-20-2018, 12:37 PM   #1
Junior Member
Location: Birmingham

Join Date: Mar 2017
Posts: 1
Default human contamination for mouse RNAseq samples

I'm working on data analysis of mouse RNAseq samples now. The library was prepared by Nugen Universal Plus mRNA-seq kit, sequenced by Illumina HiSeq 2500, single end 50bp. I mapped the reads to mm10 reference and the mapping rate was low for some samples. I checked the unmapped reads and found it can be mapped to the human genome. I summarized commands and the mapping rate as follows.

STAR --genomeDir /path/to/Mus_musculus.GRCm38_dir --readFilesIn /path/to/read1 --outFileNamePrefix /path/to/output/dir/prefix --outSAMtype BAM SortedByCoordinate Unsorted --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 100000 --alignMatesGapMax 100000

STAR --genomeDir /path/to/ENSEMBL.homo_sapiens_dir --readFilesIn /path/to/read1 --outFileNamePrefix /path/to/output/dir/prefix --outSAMtype BAM SortedByCoordinate Unsorted --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 100000 --alignMatesGapMax 100000

Sample mouse_mapping_rate human_mapping_rate
mouse_sample1 28.63% 71.87%
mouse_sample2 72.53% 41.21%
mouse_sample3 75.03% 37.65%
mouse_sample4 50.51% 55.50%
mouse_sample5 68.56% 43.18%
mouse_sample6 3.30% 90.45%
mouse_sample7 75.45% 39.63%
mouse_sample8 69.98% 42.84%
mouse_sample9 33.56% 69.02%
mouse_sample10 23.53% 78.36%
mouse_sample11 54.74% 54.65%
mouse_sample12 58.27% 50.32%
mouse_sample13 50.98% 56.36%
mouse_sample14 77.27% 37.42%
mouse_sample15 48.44% 57.53%
mouse_sample16 58.93% 50.21%
mouse_sample17 78.94% 36.84%
mouse_sample18 65.56% 44.09%

My questions are:
Could anyone know what's the overlap rate between the mouse and human transcriptome?
Whether can human contamination interfere with the analysis of mouse data?
Thanks a lot.

Last edited by cassiemin; 06-20-2018 at 01:05 PM.
cassiemin is offline   Reply With Quote
Old 06-20-2018, 02:50 PM   #2
Senior Member
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,813

Use from BBMap to separate human and mouse reads as shown in this thread.

SeqAnswers thread page for BBsplit can be found here.
GenoMax is offline   Reply With Quote
Old 06-21-2018, 02:23 PM   #3
Location: Bay Area

Join Date: Jun 2012
Posts: 94

Have you verified with your sequencing provider that they gave you the right data back? I've previously had a vender return another user's data to me. Luckily, we had used a custom protocol and it was immediately obvious something was up.
Also, check the source of your samples. One time I bought human liver FFPE that turned out to align to rat...
cmbetts is offline   Reply With Quote

human contamination, mouse rnaseq samples

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 06:26 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO