Regarding output of the file generated

[Proy321]

Hello,

I have used both bed file and gff file to do the lift-over annotation, but it ended up with a error. In case of output file generated after using the gff command (attached herewith) , it ended up with fail (no match to target assembly) in the last column of the file generated. In case of output file generated using the bed command , it also ended up with fail in the last column (attached herewith).It would be nice if you can help me with the same as what went wrong. Thanks

[liguowang]

Hello, I cannot figure out the reason unless you provide the following: 1) chain file, 2) input file, 3) output file, 4) The command and the error message. Thanks

[Proy321]

Hello, As mentioned, please find the command below and attached folder with the necessary files.

1. Command CrossMap gff GCF_000002415.2ToGCA_900093555.2.over.chain.gz PlasmoDB-63_PvivaxSal1.gff > crossmap_sal1

No such error message just " fail (no match to target assembly)" at end of column

2.Command CrossMap bed [chain] [bed] > [out_bed]

Error:- "Start coordinate is not an integer. skip chrom start end name score strand thickStart thickEnd itemRgb blockCount blockSizes blockStarts"

On Mon, Sep 16, 2024 at 7:24 PM Liguo Wang @.***> wrote:

Hello, I cannot figure out the reason unless you provide the following: 1) chain file, 2) input file, 3) output file, 4) The command and the error message. Thanks

— Reply to this email directly, view it on GitHub https://github.com/liguowang/CrossMap/issues/76#issuecomment-2352993592, or unsubscribe https://github.com/notifications/unsubscribe-auth/BBNGRYZVKXNP2EAIZLE77VTZW3PINAVCNFSM6AAAAABOJGQFKKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNJSHE4TGNJZGI . You are receiving this because you authored the thread.Message ID: @.***>

--

Priyanka Roy (2020PHXF0424P)

Ph.D. Scholar,

Department of Biological Sciences,

Birla Institute of Technology & Sciences, Pilani

Rajasthan, India-333031

Phone no.: +91-8617384648

-- The information contained in this electronic communication is intended solely for the individual(s) or entity to which it is addressed. It may contain proprietary, confidential and/or legally privileged information. Any review, retransmission, dissemination, printing, copying or other use of, or taking any action in reliance on the contents of this information by person(s) or entities other than the intended recipient is strictly prohibited and may be unlawful. If you have received this communication in error, please notify us by responding to this email or telephone and immediately and permanently delete all copies of this message and any attachments from your system(s). The contents of this message do not necessarily represent the views or policies of BITS Pilani.

[liguowang]

I did not see your attached folder. please do not send me the entire BED or GFF file, I only need the first several rows of your data to check the format. please also send me the chain file.

On Mon, Sep 16, 2024 at 10:59 AM Proy321 @.***> wrote:

Hello, As mentioned, please find the command below and attached folder with the necessary files.

1. Command CrossMap gff GCF_000002415.2ToGCA_900093555.2.over.chain.gz PlasmoDB-63_PvivaxSal1.gff > crossmap_sal1

No such error message just " fail (no match to target assembly)" at end of column

2.Command CrossMap bed [chain] [bed] > [out_bed]

Error:- "Start coordinate is not an integer. skip chrom start end name score strand thickStart thickEnd itemRgb blockCount blockSizes blockStarts"

On Mon, Sep 16, 2024 at 7:24 PM Liguo Wang @.***> wrote:

Hello, I cannot figure out the reason unless you provide the following: 1) chain file, 2) input file, 3) output file, 4) The command and the error message. Thanks

— Reply to this email directly, view it on GitHub https://github.com/liguowang/CrossMap/issues/76#issuecomment-2352993592,

or unsubscribe < https://github.com/notifications/unsubscribe-auth/BBNGRYZVKXNP2EAIZLE77VTZW3PINAVCNFSM6AAAAABOJGQFKKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNJSHE4TGNJZGI>

. You are receiving this because you authored the thread.Message ID: @.***>

--

Priyanka Roy (2020PHXF0424P)

Ph.D. Scholar,

Department of Biological Sciences,

Birla Institute of Technology & Sciences, Pilani

Rajasthan, India-333031

Phone no.: +91-8617384648

-- The information contained in this electronic communication is intended solely for the individual(s) or entity to which it is addressed. It may contain proprietary, confidential and/or legally privileged information. Any review, retransmission, dissemination, printing, copying or other use of, or taking any action in reliance on the contents of this information by person(s) or entities other than the intended recipient is strictly prohibited and may be unlawful. If you have received this communication in error, please notify us by responding to this email or telephone and immediately and permanently delete all copies of this message and any attachments from your system(s). The contents of this message do not necessarily represent the views or policies of BITS Pilani.

— Reply to this email directly, view it on GitHub https://github.com/liguowang/CrossMap/issues/76#issuecomment-2353318361, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACN443SZJ4QMFYSNCK26JM3ZW3577AVCNFSM6AAAAABOJGQFKKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNJTGMYTQMZWGE . You are receiving this because you commented.Message ID: @.***>

[Proy321]

Please find the attached chain file. GCF_000002415.2ToGCA_900093555.2.over.chain.gz

[Proy321]

Also please find the below first few rows of the gff and bed output. bed output.txt gff output.txt

Thanks

[liguowang]

The chromosome IDs do NOT match between your chain file and the BED/GFF file. The chain file uses "NC_009919.1" (contig ID?), while the BED/GFF file uses "chr".

[Proy321]

Thank you so much for your response. I will do the necessary changes in the bed file. The other query I have is regarding the gff output, what could be the reason for the error fail (no match to target assembly)" at end of column.

Thanks

[Proy321]

Hello @liguowang Even after replacing the first column of 'chr1' with NC_009919.1, it is still throwing the same error(attached herewith) New bed file.txt

"Start coordinate is not an integer. skip chrom start end name score strand thickStart thickEnd itemRgb blockCount blockSizes blockStarts"

It would be nice of you can help me with the same.