Differences between *-TCR-ALL.txt and *-TCR-ALL.fa files in trust 3.0.1

[ting...@gmail.com]

Hi,

I ran trust on my bam files and got some output files. And I am confused about the *-TCR-ALL.txt and *-TCR-ALL.fa files. Both of them have items like filename, V gene, J gene, C gene, aligner reported gene and so on. But there are still some differences between the two files. Dose the tool use some filtration standards like CDR3 length to get *-TCR-ALL.txt from the *-TCR-ALL.fa? If I want to analyse the distrubution of TRBV's CDR3 length, should I use CDR3 details from *-TCR-ALL.txt or *-TCR-ALL.fa?

I read the answer of  TRBV/TRBJ/TRBC output. But I'm still confused about the *-TCR-ALL.txt file. I thought reads were first mapped to the gene regions like TRBV and then if a read pair has one unmapped read assembled for the CDR3, and its mate is mapped to TRBC,  then trust will put TRBV in V gene. Dose the aligner reported gene do the same? If I want to get all TRBV's CDR3 length from my bam files, how should I know if the CDR3 is from TRBV? From the items V gene or Aligner reported gene? 

Best,

Ting

[Bo Li]

Hi Ting,

Could you attached the .txt and .fa files so that we can take a look?

Thanks,

Bo

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[ting...@gmail.com]

Hi, Bob

Thank you for quick reply. Please find attached the .txt and .fa files.

Best,

Ting

在 2018年6月19日星期二 UTC+8下午10:53:42，Bo Li写道：

Hi Ting,

Could you attached the .txt and .fa files so that we can take a look?

Thanks,

Bo

On Tue, Jun 19, 2018 at 7:21 AM, <ting...@gmail.com> wrote:

Hi,

I ran trust on my bam files and got some output files. And I am confused about the *-TCR-ALL.txt and *-TCR-ALL.fa files. Both of them have items like filename, V gene, J gene, C gene, aligner reported gene and so on. But there are still some differences between the two files. Dose the tool use some filtration standards like CDR3 length to get *-TCR-ALL.txt from the *-TCR-ALL.fa? If I want to analyse the distrubution of TRBV's CDR3 length, should I use CDR3 details from *-TCR-ALL.txt or *-TCR-ALL.fa?

I read the answer of  TRBV/TRBJ/TRBC output. But I'm still confused about the *-TCR-ALL.txt file. I thought reads were first mapped to the gene regions like TRBV and then if a read pair has one unmapped read assembled for the CDR3, and its mate is mapped to TRBC,  then trust will put TRBV in V gene. Dose the aligner reported gene do the same? If I want to get all TRBV's CDR3 length from my bam files, how should I know if the CDR3 is from TRBV? From the items V gene or Aligner reported gene? 

Best,

Ting

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[Bo Li]

Hi Ting,

Please use the results in the .fa file. When analyzing the partial CDR3 data, we usually recommend users to apply a length filter, for example, anything shorter than 6 amino acid should be removed. So, the two files are actually quite similar.

Best,

Bo

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[ting...@gmail.com]

Hi Bob,

Thank you very much for your help. So the .fa file contains all CDR3 data? And after I apply a length filter I will get the .txt file? It seems that the .txt file has less CDR3 data than the .fa file.

And another question please: it seems that the .fa file below can map to many TRBV genes. And I see that the aligner reported gene is TRBC1. What does that mean?

>FL_tumor_4_grch38_mapped_NODUPS.bam+est_clonal_exp=0.025641025641+contig_reads_count=1+seq_length=49+est_lib_size=3244+TRBV29-1*01_TRBV5-5*02_TRBV2*03_TRBV13*02_TRBV19*02_TRBV29-1*02_TRBV10-2*01_TRBV19*03_TRBV5-5*03_TRBV7-9*05_TRBV10-1*02_TRBV10-3*02_TRBV11-3*02_TRBV20-1*01_TRBV20-1*07_TRBV15*02_TRBV20-1*05_TRBV24-1*01_TRBV20-1*02_TRBV10-3*01_TRBV15*03_TRBV11-3*01_TRBV6-1*01_TRBV20-1*04_TRBV29-1*03_TRBV16*03_TRBV16*01_TRBV3-1*01_TRBV9*01_TRBV25-1*01_TRBV9*03_TRBV12-5*01_TRBV10-1*01_TRBV10-2*02_TRBV20-1*06_TRBV10-3*03_TRBV12-4*02_TRBV12-4*01_TRBV4-2*02_TRBV10-3*04_TRBV5-6*01_TRBV20-1*03_TRBV6-3*01_TRBV12-3*01_TRBV2*02_TRBV9*02_TRBV11-3*03_TRBV11-1*01_TRBV5-5*01_TRBV5-1*01_TRBV3-1*02_TRBV2*01_TRBV7-9*06_TRBV5-1*02_TRBV28*01_TRBV6-2*01_TRBV15*01_TRBV13*01_TRBV19*01++TRBC1|7:142791694-142792080+CSTPGLGAD+minus_log_Eval=0.05408985094468677+TGCTCTACCCCAGGCCTCGGCGCTGAC

CTCGGAAGTGAAGCCACAGTCTGCTCTACCCCAGGCCTCGGCGCTGACG

Best,

Ting

在 2018年6月21日星期四 UTC+8上午12:47:14，Bo Li写道：

[Bo Li]

Hi Ting,

The long list of TRBV genes were obtained from alignment using contigs assembled in TRUST, while TRBC gene is called based on the paired-end alignment performed by the aligner. We usually trust the aligner report better, as the contigs from de novo assembly are usually short, and cannot be uniquely mapped to one V gene.

Thanks,

Bo

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[ting...@gmail.com]

That's helpful. Thank you, Bo.

在 2018年6月21日星期四 UTC+8上午9:59:23，Bo Li写道：