What are these BC files for? Should I use them in alignment?

samhokin · 06-24-2019, 08:21 AM

Hi, folks. I've started working with some old SOLiD single-ended RNA-seq reads, from 2010 and 2011. I'm using novoalignCS and have the quality files, csfasta files, and an additional fasta-like file with "BC" in the filename. Here's an example of the filenames:

S1001938CIS_7/primary.20100713155754122/reads/

solid0015_20100706_S1001938CIS_BC_bcSample1_F3.csfasta
solid0015_20100706_S1001938CIS_BC_bcSample1_F3.stats
solid0015_20100706_S1001938CIS_BC_bcSample1_F3_QV.qual

S1001938CIS_7/primary.20100707172116543/reads/

solid0015_20100706_S1001938CIS_BC_bcSample1_BC.csfasta

The F3.csfasta and F3_QV.qual files are as expected, and work fine with novoalignCS.

The BC.csfasta files have data as follows and I'm completely mystified as to what they are:

# Wed Jul 7 11:02:39 2010 /share/apps/corona/bin/filter_fasta.pl --output=/data/results/solid0015/solid0015_20100706_S1001938CIS_BC/bcSample1/results.F1B1/primary.20100707172116543 --name=solid0015_20100706_S1001938CIS_BC_bcSample1 --tag=BC --minlength=5 --mincalls=25 --prefix=G /data/results/solid0015/solid0015_20100706_S1001938CIS_BC/bcSample1/jobs/postPrimerSetPrimary.1505/rawseq
# Cwd: /home/pipeline
# Title: solid0015_20100706_S1001938CIS_BC_bcSample1
# Library:S1001938CIS_7:00313
>1_223_2_BC 0
G00313
>1_238_37_BC 0
G00313
>1_240_14_BC 0
G00313

Anyone know? Should I be using these BC files in some way? They have extremely little information content.

colindaven · 07-11-2019, 06:38 AM

Well, the main thing is your csfasta and qual files work fine.

Could BC be barcode ? They seemt to be short, as in barcodes, and the format seems to be the csfasta format.

Not sure I ever saw these in my days of SOLiD adventures, which ended in 2012 (thank god).

mrsrankind1990 · 03-27-2020, 10:04 AM

Quote:

Originally Posted by colindaven

Well, the main thing is your csfasta and qual files work fine.

Could BC be barcode ? They seemt to be short, as in barcodes, and the format seems to be the csfasta format.

Not sure I ever saw these in my days of SOLiD adventures, which ended in 2012 (thank god).

God damn you are right. 2012 HAHA

samhokin · 03-27-2020, 10:39 AM

Hey, the data turned out OK and was useful! But yeah, I had to dust off the hard drive the reads were on, it'd been sitting on a shelf for eight years or so.

awhite95 · 02-24-2021, 07:24 AM

wow that is some really good work that you've been doing there. I had been closely associated with some projects on Encodeproject on RNA sequence measures.

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06-24-2019, 08:21 AM	#1
samhokin Member Location: Santa Fe, NM Join Date: Nov 2013 Posts: 20	What are these BC files for? Should I use them in alignment? Hi, folks. I've started working with some old SOLiD single-ended RNA-seq reads, from 2010 and 2011. I'm using novoalignCS and have the quality files, csfasta files, and an additional fasta-like file with "BC" in the filename. Here's an example of the filenames: S1001938CIS_7/primary.20100713155754122/reads/ solid0015_20100706_S1001938CIS_BC_bcSample1_F3.csfasta solid0015_20100706_S1001938CIS_BC_bcSample1_F3.stats solid0015_20100706_S1001938CIS_BC_bcSample1_F3_QV.qual S1001938CIS_7/primary.20100707172116543/reads/ solid0015_20100706_S1001938CIS_BC_bcSample1_BC.csfasta The F3.csfasta and F3_QV.qual files are as expected, and work fine with novoalignCS. The BC.csfasta files have data as follows and I'm completely mystified as to what they are: # Wed Jul 7 11:02:39 2010 /share/apps/corona/bin/filter_fasta.pl --output=/data/results/solid0015/solid0015_20100706_S1001938CIS_BC/bcSample1/results.F1B1/primary.20100707172116543 --name=solid0015_20100706_S1001938CIS_BC_bcSample1 --tag=BC --minlength=5 --mincalls=25 --prefix=G /data/results/solid0015/solid0015_20100706_S1001938CIS_BC/bcSample1/jobs/postPrimerSetPrimary.1505/rawseq # Cwd: /home/pipeline # Title: solid0015_20100706_S1001938CIS_BC_bcSample1 # Library:S1001938CIS_7:00313 >1_223_2_BC 0 G00313 >1_238_37_BC 0 G00313 >1_240_14_BC 0 G00313 Anyone know? Should I be using these BC files in some way? They have extremely little information content. __________________ Sam Hokin Computational Scientist, Carnegie and NCGR

03-27-2020, 10:39 AM	#4
samhokin Member Location: Santa Fe, NM Join Date: Nov 2013 Posts: 20	Hey, the data turned out OK and was useful! But yeah, I had to dust off the hard drive the reads were on, it'd been sitting on a shelf for eight years or so. __________________ Sam Hokin Computational Scientist, Carnegie and NCGR

02-24-2021, 07:24 AM	#5
awhite95 Junior Member Location: United States Join Date: Feb 2021 Posts: 2	wow that is some really good work that you've been doing there. I had been closely associated with some projects on Encodeproject on RNA sequence measures. __________________ "Anyone who has never made a mistake, has never learnt anything new" - Albert Einstein I work as a consultant and research analyst at eduhelphub

07-11-2019, 06:38 AM	#2
colindaven Senior Member Location: Germany Join Date: Oct 2008 Posts: 415	Well, the main thing is your csfasta and qual files work fine. Could BC be barcode ? They seemt to be short, as in barcodes, and the format seems to be the csfasta format. Not sure I ever saw these in my days of SOLiD adventures, which ended in 2012 (thank god).